Sun 21 Oct 09:15:25 BST 2018: starting 22752: build of rdkit version 201709.3+dfsg-1 arch armhf on maul Running apt-get -q --download-only --only-source source rdkit=201709.3+dfsg-1 Reading package lists... NOTICE: 'rdkit' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debichem/packages/rdkit.git Please use: git clone https://anonscm.debian.org/git/debichem/packages/rdkit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 24.5 MB of source archives. Get:1 http://mirror/debian unstable/main rdkit 201709.3+dfsg-1 (dsc) [2,579 B] Get:2 http://mirror/debian unstable/main rdkit 201709.3+dfsg-1 (tar) [24.5 MB] Get:3 http://mirror/debian unstable/main rdkit 201709.3+dfsg-1 (diff) [8,044 B] Fetched 24.5 MB in 1s (19.2 MB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rdkit_201709.3+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) total 23976 -rw-r--r-- 1 root root 8044 Mar 26 2018 rdkit_201709.3+dfsg-1.debian.tar.xz -rw-r--r-- 1 root root 2579 Mar 26 2018 rdkit_201709.3+dfsg-1.dsc -rw-r--r-- 1 root root 24535224 Mar 26 2018 rdkit_201709.3+dfsg.orig.tar.xz sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on maul.einval.org +==============================================================================+ | rdkit 201709.3+dfsg-1 (armhf) Sun, 21 Oct 2018 08:15:27 +0000 | +==============================================================================+ Package: rdkit Version: 201709.3+dfsg-1 Source Version: 201709.3+dfsg-1 Distribution: sid Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-armhf-sbuild-41abf9f1-612a-4bfc-9398-04d81a39e514' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [233 kB] Ign:2 http://mirror.einval.org/debian sid/main armhf Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main armhf Packages.diff/Index [27.9 kB] Ign:2 http://mirror.einval.org/debian sid/main armhf Packages.diff/Index Get:3 http://mirror.einval.org/debian sid/main armhf Packages [7988 kB] Fetched 8220 kB in 3s (3177 kB/s) Reading package lists... Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: libgdbm6 The following packages will be upgraded: binutils binutils-arm-linux-gnueabihf binutils-common cpp-8 dpkg dpkg-dev g++-8 gcc-8 gcc-8-base gpgv libasan5 libatomic1 libbinutils libcc1-0 libdpkg-perl libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libgpg-error0 libncursesw6 libperl5.26 libstdc++-8-dev libstdc++6 libtinfo6 libubsan1 linux-libc-dev ncurses-base ncurses-bin perl perl-base sed sysvinit-utils tzdata 34 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 38.9 MB of archives. After this operation, 380 kB disk space will be freed. Get:1 http://mirror.einval.org/debian sid/main armhf dpkg armhf 1.19.2 [2094 kB] Get:2 http://mirror.einval.org/debian sid/main armhf ncurses-bin armhf 6.1+20181013-1 [398 kB] Get:3 http://mirror.einval.org/debian sid/main armhf libgdbm6 armhf 1.18-2 [60.4 kB] Get:4 http://mirror.einval.org/debian sid/main armhf libgdbm-compat4 armhf 1.18-2 [42.9 kB] Get:5 http://mirror.einval.org/debian sid/main armhf perl-base armhf 5.26.2-7+b1 [1297 kB] Get:6 http://mirror.einval.org/debian sid/main armhf perl armhf 5.26.2-7+b1 [202 kB] Get:7 http://mirror.einval.org/debian sid/main armhf libperl5.26 armhf 5.26.2-7+b1 [2940 kB] Get:8 http://mirror.einval.org/debian sid/main armhf sed armhf 4.5-2 [288 kB] Get:9 http://mirror.einval.org/debian sid/main armhf ncurses-base all 6.1+20181013-1 [258 kB] Get:10 http://mirror.einval.org/debian sid/main armhf sysvinit-utils armhf 2.88dsf-59.11 [67.0 kB] Get:11 http://mirror.einval.org/debian sid/main armhf libgpg-error0 armhf 1.32-3 [60.7 kB] Get:12 http://mirror.einval.org/debian sid/main armhf gpgv armhf 2.2.10-3 [548 kB] Get:13 http://mirror.einval.org/debian sid/main armhf libcc1-0 armhf 8.2.0-8 [31.0 kB] Get:14 http://mirror.einval.org/debian sid/main armhf libgomp1 armhf 8.2.0-8 [64.7 kB] Get:15 http://mirror.einval.org/debian sid/main armhf libatomic1 armhf 8.2.0-8 [6756 B] Get:16 http://mirror.einval.org/debian sid/main armhf libasan5 armhf 8.2.0-8 [336 kB] Get:17 http://mirror.einval.org/debian sid/main armhf libubsan1 armhf 8.2.0-8 [105 kB] Get:18 http://mirror.einval.org/debian sid/main armhf gcc-8-base armhf 8.2.0-8 [187 kB] Get:19 http://mirror.einval.org/debian sid/main armhf libstdc++6 armhf 8.2.0-8 [338 kB] Get:20 http://mirror.einval.org/debian sid/main armhf g++-8 armhf 8.2.0-8 [6078 kB] Get:21 http://mirror.einval.org/debian sid/main armhf libstdc++-8-dev armhf 8.2.0-8 [1574 kB] Get:22 http://mirror.einval.org/debian sid/main armhf libgcc-8-dev armhf 8.2.0-8 [613 kB] Get:23 http://mirror.einval.org/debian sid/main armhf gcc-8 armhf 8.2.0-8 [5979 kB] Get:24 http://mirror.einval.org/debian sid/main armhf cpp-8 armhf 8.2.0-8 [5604 kB] Get:25 http://mirror.einval.org/debian sid/main armhf libgcc1 armhf 1:8.2.0-8 [37.1 kB] Get:26 http://mirror.einval.org/debian sid/main armhf libbinutils armhf 2.31.1-7 [302 kB] Get:27 http://mirror.einval.org/debian sid/main armhf binutils-common armhf 2.31.1-7 [2071 kB] Get:28 http://mirror.einval.org/debian sid/main armhf binutils armhf 2.31.1-7 [55.9 kB] Get:29 http://mirror.einval.org/debian sid/main armhf binutils-arm-linux-gnueabihf armhf 2.31.1-7 [2094 kB] Get:30 http://mirror.einval.org/debian sid/main armhf libtinfo6 armhf 6.1+20181013-1 [312 kB] Get:31 http://mirror.einval.org/debian sid/main armhf libncursesw6 armhf 6.1+20181013-1 [105 kB] Get:32 http://mirror.einval.org/debian sid/main armhf tzdata all 2018f-1 [254 kB] Get:33 http://mirror.einval.org/debian sid/main armhf dpkg-dev all 1.19.2 [1608 kB] Get:34 http://mirror.einval.org/debian sid/main armhf libdpkg-perl all 1.19.2 [1374 kB] Get:35 http://mirror.einval.org/debian sid/main armhf linux-libc-dev armhf 4.18.10-2 [1519 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.9 MB in 1s (47.7 MB/s) (Reading database ... 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Preparing to unpack .../libdpkg-perl_1.19.2_all.deb ... Unpacking libdpkg-perl (1.19.2) over (1.19.1) ... Preparing to unpack .../linux-libc-dev_4.18.10-2_armhf.deb ... Unpacking linux-libc-dev:armhf (4.18.10-2) over (4.18.6-1) ... Setting up cpp-8 (8.2.0-8) ... Setting up libgomp1:armhf (8.2.0-8) ... Setting up libatomic1:armhf (8.2.0-8) ... Setting up libcc1-0:armhf (8.2.0-8) ... Setting up tzdata (2018f-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Oct 21 08:16:17 UTC 2018. Universal Time is now: Sun Oct 21 08:16:17 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up linux-libc-dev:armhf (4.18.10-2) ... Setting up libgdbm6:armhf (1.18-2) ... Setting up binutils-common:armhf (2.31.1-7) ... Processing triggers for libc-bin (2.27-6) ... Setting up libgdbm-compat4:armhf (1.18-2) ... Setting up libasan5:armhf (8.2.0-8) ... Setting up libubsan1:armhf (8.2.0-8) ... Setting up libbinutils:armhf (2.31.1-7) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-7) ... Setting up libperl5.26:armhf (5.26.2-7+b1) ... Setting up libgcc-8-dev:armhf (8.2.0-8) ... Setting up binutils (2.31.1-7) ... Setting up libstdc++-8-dev:armhf (8.2.0-8) ... Setting up gcc-8 (8.2.0-8) ... Setting up perl (5.26.2-7+b1) ... Setting up g++-8 (8.2.0-8) ... Setting up libdpkg-perl (1.19.2) ... Setting up dpkg-dev (1.19.2) ... Processing triggers for libc-bin (2.27-6) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /chroot/rebuildd/build-rdkit/rdkit_201709.3+dfsg-1.dsc exists in /chroot/rebuildd/build-rdkit; copying to chroot I: NOTICE: Log filtering will replace 'build/rdkit-DmlRE5/rdkit-201709.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rdkit-DmlRE5' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-4w4sLx/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-4w4sLx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4w4sLx/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-4w4sLx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4w4sLx/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-4w4sLx/apt_archive ./ Packages [430 B] Fetched 1736 B in 0s (115 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 848 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-4w4sLx/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 848 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11478 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: bison, cmake, debhelper (>> 9), dh-python, doxygen, flex, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libsqlite3-dev, latexmk, pandoc, python-dev, python-epydoc, python-pil, python-numpy, python-pandas, python3-sphinx, python3-recommonmark, texlive-fonts-recommended, texlive-generic-extra, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended Filtered Build-Depends: bison, cmake, debhelper (>> 9), dh-python, doxygen, flex, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libsqlite3-dev, latexmk, pandoc, python-dev, python-epydoc, python-pil, python-numpy, python-pandas, python3-sphinx, python3-recommonmark, texlive-fonts-recommended, texlive-generic-extra, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended dpkg-deb: building package 'sbuild-build-depends-rdkit-dummy' in '/<>/resolver-4w4sLx/apt_archive/sbuild-build-depends-rdkit-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-rdkit-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-4w4sLx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4w4sLx/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-4w4sLx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4w4sLx/apt_archive ./ Sources [642 B] Get:5 copy:/<>/resolver-4w4sLx/apt_archive ./ Packages [722 B] Fetched 2327 B in 0s (148 kB/s) Reading package lists... Reading package lists... Install rdkit build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bison bsdmainutils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common doxygen dwz file flex fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian latexmk libarchive-zip-perl libarchive13 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas3 libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-dev libboost-python-dev libboost-python1.62-dev libboost-python1.62.0 libboost-regex-dev libboost-regex1.62-dev libboost-regex1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost1.62-dev libbrotli1 libbsd0 libcairo2 libclang1-6.0 libcroco3 libcups2 libcupsimage2 libcurl4 libdbus-1-3 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm6.0 liblua5.1-0 liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libprocps7 libpsl5 libptexenc1 libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libreadline7 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libsqlite3-dev libssh2-1 libssl1.1 libsynctex2 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuv1 libwebp6 libwebpdemux2 libwebpmux3 libwoff1 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libyaml-0-2 libzzip-0-13 lsb-base m4 man-db mime-support openssl pandoc pandoc-data pkg-config po-debconf poppler-data preview-latex-style procps python python-babel-localedata python-dateutil python-dev python-epydoc python-minimal python-numpy python-pandas python-pandas-lib python-pil python-pkg-resources python-six python-tz python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-commonmark-bkrs python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-recommonmark python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3.6 python3.6-dev python3.6-minimal readline-common sensible-utils sgml-base sphinx-common t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-generic-extra texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic ucf x11-common xdg-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui graphviz flex-doc gettext-doc libasprintf-dev libgettextpo-dev groff ghostscript lrzip libboost-doc libboost1.62-doc gccxml libboost-context1.62-dev libboost-coroutine1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-random1.62-dev libboost-signals1.62-dev libboost-test1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev cups-common libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils libgraphite2-utils krb5-doc krb5-user icu-doc liblcms2-utils sqlite3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser texlive-xetex texlive-luatex pandoc-citeproc context wkhtmltopdf librsvg2-bin ghc nodejs php ruby r-base-core libjs-mathjax node-katex libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk epydoc-doc gfortran python-nose python-numpy-dbg python-numpy-doc python-pandas-doc python-pil-doc python-pil-dbg python-setuptools python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python-commonmark-bkrs-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french python-jinja2-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks dvipng imagemagick-6.q16 python3-sphinx-rtd-theme python3-stemmer sphinx-doc python3.6-venv python3.6-doc readline-doc sgml-base-doc gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer texlive-fonts-recommended-doc texlive-latex-base-doc python-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex Recommended packages: libfl-dev curl | wget | lynx xpdf-reader | pdf-viewer gv | postscript-viewer libcupsfilters1 dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs fonts-droid-fallback javascript-common krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc python-tk python-docutils graphviz python-scipy python-matplotlib python-tables python-numexpr python-xlrd python-statsmodels python-openpyxl python-xlwt python-bs4 python-html5lib python-lxml python-olefile python3-pil lmodern tex-gyre tipa ruby | ruby-interpreter tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison bsdmainutils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common doxygen dwz file flex fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian latexmk libarchive-zip-perl libarchive13 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas3 libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-dev libboost-python-dev libboost-python1.62-dev libboost-python1.62.0 libboost-regex-dev libboost-regex1.62-dev libboost-regex1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost1.62-dev libbrotli1 libbsd0 libcairo2 libclang1-6.0 libcroco3 libcups2 libcupsimage2 libcurl4 libdbus-1-3 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm6.0 liblua5.1-0 liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libopenjp2-7 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libprocps7 libpsl5 libptexenc1 libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libreadline7 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libsqlite3-dev libssh2-1 libssl1.1 libsynctex2 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuv1 libwebp6 libwebpdemux2 libwebpmux3 libwoff1 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libyaml-0-2 libzzip-0-13 lsb-base m4 man-db mime-support openssl pandoc pandoc-data pkg-config po-debconf poppler-data preview-latex-style procps python python-babel-localedata python-dateutil python-dev python-epydoc python-minimal python-numpy python-pandas python-pandas-lib python-pil python-pkg-resources python-six python-tz python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-commonmark-bkrs python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-recommonmark python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3.6 python3.6-dev python3.6-minimal readline-common sbuild-build-depends-rdkit-dummy sensible-utils sgml-base sphinx-common t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-generic-extra texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic ucf x11-common xdg-utils xml-core zlib1g-dev 0 upgraded, 271 newly installed, 0 to remove and 0 not upgraded. Need to get 314 MB of archives. After this operation, 1087 MB of additional disk space will be used. 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[22.7 kB] Get:23 http://mirror.einval.org/debian sid/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get:24 http://mirror.einval.org/debian sid/main armhf m4 armhf 1.4.18-1 [191 kB] Get:25 http://mirror.einval.org/debian sid/main armhf flex armhf 2.6.4-6.2 [438 kB] Get:26 http://mirror.einval.org/debian sid/main armhf poppler-data all 0.4.9-2 [1473 kB] Get:27 http://mirror.einval.org/debian sid/main armhf libpython3.6-minimal armhf 3.6.7~rc2-1 [566 kB] Get:28 http://mirror.einval.org/debian sid/main armhf python3.6-minimal armhf 3.6.7~rc2-1 [1384 kB] Get:29 http://mirror.einval.org/debian sid/main armhf python3-minimal armhf 3.6.6-1 [36.4 kB] Get:30 http://mirror.einval.org/debian sid/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get:31 http://mirror.einval.org/debian sid/main armhf libpython3.6-stdlib armhf 3.6.7~rc2-1 [1634 kB] Get:32 http://mirror.einval.org/debian sid/main armhf python3.6 armhf 3.6.7~rc2-1 [240 kB] Get:33 http://mirror.einval.org/debian sid/main armhf libpython3-stdlib armhf 3.6.6-1 [19.8 kB] Get:34 http://mirror.einval.org/debian sid/main armhf python3 armhf 3.6.6-1 [47.5 kB] Get:35 http://mirror.einval.org/debian sid/main armhf sgml-base all 1.29 [14.8 kB] Get:36 http://mirror.einval.org/debian sid/main armhf sensible-utils all 0.0.12 [15.8 kB] Get:37 http://mirror.einval.org/debian sid/main armhf ucf all 3.0038 [67.8 kB] Get:38 http://mirror.einval.org/debian sid/main armhf tex-common all 6.10 [53.0 kB] Get:39 http://mirror.einval.org/debian sid/main armhf libncurses6 armhf 6.1+20181013-1 [79.6 kB] Get:40 http://mirror.einval.org/debian sid/main armhf libprocps7 armhf 2:3.3.15-2 [58.7 kB] Get:41 http://mirror.einval.org/debian sid/main armhf lsb-base all 9.20170808 [28.1 kB] Get:42 http://mirror.einval.org/debian sid/main armhf procps armhf 2:3.3.15-2 [248 kB] Get:43 http://mirror.einval.org/debian sid/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB] Get:44 http://mirror.einval.org/debian sid/main armhf libmagic1 armhf 1:5.34-2 [108 kB] Get:45 http://mirror.einval.org/debian sid/main armhf file armhf 1:5.34-2 [64.9 kB] Get:46 http://mirror.einval.org/debian sid/main armhf gettext-base armhf 0.19.8.1-8 [118 kB] Get:47 http://mirror.einval.org/debian sid/main armhf autoconf all 2.69-11 [341 kB] Get:48 http://mirror.einval.org/debian sid/main armhf autotools-dev all 20180224.1 [77.0 kB] Get:49 http://mirror.einval.org/debian sid/main armhf automake all 1:1.16.1-1.1 [771 kB] Get:50 http://mirror.einval.org/debian sid/main armhf autopoint all 0.19.8.1-8 [434 kB] Get:51 http://mirror.einval.org/debian sid/main armhf libbison-dev armhf 2:3.0.4.dfsg-1+b1 [433 kB] Get:52 http://mirror.einval.org/debian sid/main armhf bison armhf 2:3.0.4.dfsg-1+b1 [765 kB] Get:53 http://mirror.einval.org/debian sid/main armhf openssl armhf 1.1.1-1 [809 kB] Get:54 http://mirror.einval.org/debian sid/main armhf ca-certificates all 20180409 [161 kB] Get:55 http://mirror.einval.org/debian sid/main armhf cmake-data all 3.12.3-2 [1437 kB] Get:56 http://mirror.einval.org/debian sid/main armhf liblzo2-2 armhf 2.10-0.1 [49.7 kB] Get:57 http://mirror.einval.org/debian sid/main armhf libpng16-16 armhf 1.6.34-2 [271 kB] Get:58 http://mirror.einval.org/debian sid/main armhf libfreetype6 armhf 2.8.1-2 [406 kB] Get:59 http://mirror.einval.org/debian sid/main armhf libglib2.0-0 armhf 2.58.1-2 [1072 kB] Get:60 http://mirror.einval.org/debian sid/main armhf libgraphite2-3 armhf 1.3.12-1 [69.8 kB] Get:61 http://mirror.einval.org/debian sid/main armhf libharfbuzz0b armhf 1.9.0-1 [887 kB] Get:62 http://mirror.einval.org/debian sid/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.7 kB] Get:63 http://mirror.einval.org/debian sid/main armhf libicu60 armhf 60.2-6 [7818 kB] Get:64 http://mirror.einval.org/debian sid/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [630 kB] Get:65 http://mirror.einval.org/debian sid/main armhf libarchive13 armhf 3.2.2-5 [271 kB] Get:66 http://mirror.einval.org/debian sid/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.0 kB] Get:67 http://mirror.einval.org/debian sid/main armhf libkrb5support0 armhf 1.16.1-1 [59.2 kB] Get:68 http://mirror.einval.org/debian sid/main armhf libk5crypto3 armhf 1.16.1-1 [119 kB] Get:69 http://mirror.einval.org/debian sid/main armhf libkrb5-3 armhf 1.16.1-1 [271 kB] Get:70 http://mirror.einval.org/debian sid/main armhf libgssapi-krb5-2 armhf 1.16.1-1 [137 kB] Get:71 http://mirror.einval.org/debian sid/main armhf libsasl2-modules-db armhf 2.1.27~rc8-1 [66.7 kB] Get:72 http://mirror.einval.org/debian sid/main armhf libsasl2-2 armhf 2.1.27~rc8-1 [97.9 kB] Get:73 http://mirror.einval.org/debian sid/main armhf libldap-common all 2.4.46+dfsg-5 [88.3 kB] Get:74 http://mirror.einval.org/debian sid/main armhf libldap-2.4-2 armhf 2.4.46+dfsg-5 [200 kB] Get:75 http://mirror.einval.org/debian sid/main armhf libnghttp2-14 armhf 1.34.0-1 [74.1 kB] Get:76 http://mirror.einval.org/debian sid/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get:77 http://mirror.einval.org/debian sid/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get:78 http://mirror.einval.org/debian sid/main armhf libssh2-1 armhf 1.8.0-2 [128 kB] Get:79 http://mirror.einval.org/debian sid/main armhf libcurl4 armhf 7.61.0-1 [286 kB] Get:80 http://mirror.einval.org/debian sid/main armhf libjsoncpp1 armhf 1.7.4-3 [67.8 kB] Get:81 http://mirror.einval.org/debian sid/main armhf librhash0 armhf 1.3.6-2 [101 kB] Get:82 http://mirror.einval.org/debian sid/main armhf libuv1 armhf 1.23.1-1 [95.2 kB] Get:83 http://mirror.einval.org/debian sid/main armhf cmake armhf 3.12.3-2 [2806 kB] Get:84 http://mirror.einval.org/debian sid/main armhf libtool all 2.4.6-6 [547 kB] Get:85 http://mirror.einval.org/debian sid/main armhf dh-autoreconf all 19 [16.9 kB] Get:86 http://mirror.einval.org/debian sid/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get:87 http://mirror.einval.org/debian sid/main armhf libfile-stripnondeterminism-perl all 0.043-2 [20.2 kB] Get:88 http://mirror.einval.org/debian sid/main armhf dh-strip-nondeterminism all 0.043-2 [12.2 kB] Get:89 http://mirror.einval.org/debian sid/main armhf libelf1 armhf 0.170-0.5 [160 kB] Get:90 http://mirror.einval.org/debian sid/main armhf dwz armhf 0.12-2 [73.4 kB] Get:91 http://mirror.einval.org/debian sid/main armhf libcroco3 armhf 0.6.12-2 [133 kB] Get:92 http://mirror.einval.org/debian sid/main armhf gettext armhf 0.19.8.1-8 [1240 kB] Get:93 http://mirror.einval.org/debian sid/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:94 http://mirror.einval.org/debian sid/main armhf po-debconf all 1.0.20 [247 kB] Get:95 http://mirror.einval.org/debian sid/main armhf debhelper all 11.4.1 [989 kB] Get:96 http://mirror.einval.org/debian sid/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB] Get:97 http://mirror.einval.org/debian sid/main armhf python3-distutils all 3.6.6-1 [144 kB] Get:98 http://mirror.einval.org/debian sid/main armhf dh-python all 3.20180927 [95.8 kB] Get:99 http://mirror.einval.org/debian sid/main armhf xml-core all 0.18 [23.4 kB] Get:100 http://mirror.einval.org/debian sid/main armhf docutils-common all 0.14+dfsg-3 [204 kB] Get:101 http://mirror.einval.org/debian sid/main armhf libedit2 armhf 3.1-20180525-1 [71.9 kB] Get:102 http://mirror.einval.org/debian sid/main armhf libllvm6.0 armhf 1:6.0.1-9.1 [13.1 MB] Get:103 http://mirror.einval.org/debian sid/main armhf libclang1-6.0 armhf 1:6.0.1-9.1 [6033 kB] Get:104 http://mirror.einval.org/debian sid/main armhf libxapian30 armhf 1.4.7-4 [975 kB] Get:105 http://mirror.einval.org/debian sid/main armhf doxygen armhf 1.8.13-10 [3568 kB] Get:106 http://mirror.einval.org/debian sid/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get:107 http://mirror.einval.org/debian sid/main armhf fontconfig-config all 2.13.1-1 [280 kB] Get:108 http://mirror.einval.org/debian sid/main armhf fonts-lmodern all 2.004.5-5 [4539 kB] Get:109 http://mirror.einval.org/debian sid/main armhf libgirepository-1.0-1 armhf 1.58.0-1 [79.9 kB] Get:110 http://mirror.einval.org/debian sid/main armhf gir1.2-glib-2.0 armhf 1.58.0-1 [143 kB] Get:111 http://mirror.einval.org/debian sid/main armhf libharfbuzz-gobject0 armhf 1.9.0-1 [657 kB] Get:112 http://mirror.einval.org/debian sid/main armhf gir1.2-harfbuzz-0.0 armhf 1.9.0-1 [664 kB] Get:113 http://mirror.einval.org/debian sid/main armhf icu-devtools armhf 60.2-6 [172 kB] Get:114 http://mirror.einval.org/debian sid/main armhf libpaper1 armhf 1.1.24+nmu5 [20.9 kB] Get:115 http://mirror.einval.org/debian sid/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.3 kB] Get:116 http://mirror.einval.org/debian sid/main armhf libkpathsea6 armhf 2018.20180907.48586-2 [156 kB] Get:117 http://mirror.einval.org/debian sid/main armhf libptexenc1 armhf 2018.20180907.48586-2 [58.0 kB] Get:118 http://mirror.einval.org/debian sid/main armhf libsynctex2 armhf 2018.20180907.48586-2 [67.3 kB] Get:119 http://mirror.einval.org/debian sid/main armhf libtexlua52 armhf 2018.20180907.48586-2 [86.5 kB] Get:120 http://mirror.einval.org/debian sid/main armhf libtexlua53 armhf 2018.20180907.48586-2 [98.2 kB] Get:121 http://mirror.einval.org/debian sid/main armhf libtexluajit2 armhf 2018.20180907.48586-2 [201 kB] Get:122 http://mirror.einval.org/debian sid/main armhf t1utils armhf 1.41-2 [54.3 kB] Get:123 http://mirror.einval.org/debian sid/main armhf libbrotli1 armhf 1.0.6-1 [259 kB] Get:124 http://mirror.einval.org/debian sid/main armhf libfontconfig1 armhf 2.13.1-1 [328 kB] Get:125 http://mirror.einval.org/debian sid/main armhf libpixman-1-0 armhf 0.34.0-2 [457 kB] Get:126 http://mirror.einval.org/debian sid/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get:127 http://mirror.einval.org/debian sid/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get:128 http://mirror.einval.org/debian sid/main armhf libxcb1 armhf 1.13.1-1 [132 kB] Get:129 http://mirror.einval.org/debian sid/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get:130 http://mirror.einval.org/debian sid/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get:131 http://mirror.einval.org/debian sid/main armhf libxcb-render0 armhf 1.13.1-1 [108 kB] Get:132 http://mirror.einval.org/debian sid/main armhf libxcb-shm0 armhf 1.13.1-1 [99.0 kB] Get:133 http://mirror.einval.org/debian sid/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get:134 http://mirror.einval.org/debian sid/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get:135 http://mirror.einval.org/debian sid/main armhf libcairo2 armhf 1.16.0-1 [616 kB] Get:136 http://mirror.einval.org/debian sid/main armhf libgs9-common all 9.25~dfsg-4 [5134 kB] Get:137 http://mirror.einval.org/debian sid/main armhf libavahi-common-data armhf 0.7-4+b1 [122 kB] Get:138 http://mirror.einval.org/debian sid/main armhf libavahi-common3 armhf 0.7-4+b1 [51.1 kB] Get:139 http://mirror.einval.org/debian sid/main armhf libdbus-1-3 armhf 1.12.10-1 [188 kB] Get:140 http://mirror.einval.org/debian sid/main armhf libavahi-client3 armhf 0.7-4+b1 [54.5 kB] Get:141 http://mirror.einval.org/debian sid/main armhf libcups2 armhf 2.2.8-5 [289 kB] Get:142 http://mirror.einval.org/debian sid/main armhf libcupsimage2 armhf 2.2.8-5 [129 kB] Get:143 http://mirror.einval.org/debian sid/main armhf libidn11 armhf 1.33-2.2 [113 kB] Get:144 http://mirror.einval.org/debian sid/main armhf libijs-0.35 armhf 0.35-13 [16.9 kB] Get:145 http://mirror.einval.org/debian sid/main armhf libjbig2dec0 armhf 0.15-1 [56.8 kB] Get:146 http://mirror.einval.org/debian sid/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get:147 http://mirror.einval.org/debian sid/main armhf liblcms2-2 armhf 2.9-3 [119 kB] Get:148 http://mirror.einval.org/debian sid/main armhf libopenjp2-7 armhf 2.3.0-1 [146 kB] Get:149 http://mirror.einval.org/debian sid/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get:150 http://mirror.einval.org/debian sid/main armhf libtiff5 armhf 4.0.9-6 [228 kB] Get:151 http://mirror.einval.org/debian sid/main armhf libgs9 armhf 9.25~dfsg-4 [1892 kB] Get:152 http://mirror.einval.org/debian sid/main armhf libharfbuzz-icu0 armhf 1.9.0-1 [650 kB] Get:153 http://mirror.einval.org/debian sid/main armhf x11-common all 1:7.7+19 [251 kB] Get:154 http://mirror.einval.org/debian sid/main armhf libice6 armhf 2:1.0.9-2 [51.7 kB] Get:155 http://mirror.einval.org/debian sid/main armhf libpotrace0 armhf 1.15-1 [23.9 kB] Get:156 http://mirror.einval.org/debian sid/main armhf libsm6 armhf 2:1.2.2-1+b3 [31.3 kB] Get:157 http://mirror.einval.org/debian sid/main armhf libwoff1 armhf 1.0.2-1 [35.8 kB] Get:158 http://mirror.einval.org/debian sid/main armhf libxt6 armhf 1:1.1.5-1 [158 kB] Get:159 http://mirror.einval.org/debian sid/main armhf libxmu6 armhf 2:1.1.2-2 [52.5 kB] Get:160 http://mirror.einval.org/debian sid/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get:161 http://mirror.einval.org/debian sid/main armhf libxaw7 armhf 2:1.0.13-1+b2 [167 kB] Get:162 http://mirror.einval.org/debian sid/main armhf libxi6 armhf 2:1.7.9-1 [78.4 kB] Get:163 http://mirror.einval.org/debian sid/main armhf libxxhash0 armhf 0.6.5-1 [9920 B] Get:164 http://mirror.einval.org/debian sid/main armhf libzzip-0-13 armhf 0.13.62-3.1 [51.6 kB] Get:165 http://mirror.einval.org/debian sid/main armhf texlive-binaries armhf 2018.20180907.48586-2 [8909 kB] Get:166 http://mirror.einval.org/debian sid/main armhf xdg-utils all 1.1.3-1 [73.3 kB] Get:167 http://mirror.einval.org/debian sid/main armhf texlive-base all 2018.20181009-1 [19.0 MB] Get:168 http://mirror.einval.org/debian sid/main armhf texlive-latex-base all 2018.20181009-1 [984 kB] Get:169 http://mirror.einval.org/debian sid/main armhf latexmk all 1:4.60-0.1 [377 kB] Get:170 http://mirror.einval.org/debian sid/main armhf libgfortran5 armhf 8.2.0-8 [211 kB] Get:171 http://mirror.einval.org/debian sid/main armhf libblas3 armhf 3.8.0-1+b1 [109 kB] Get:172 http://mirror.einval.org/debian sid/main armhf libboost1.62-dev armhf 1.62.0+dfsg-10 [7003 kB] Get:173 http://mirror.einval.org/debian sid/main armhf libboost-atomic1.62.0 armhf 1.62.0+dfsg-10 [31.1 kB] Get:174 http://mirror.einval.org/debian sid/main armhf libboost-atomic1.62-dev armhf 1.62.0+dfsg-10 [30.2 kB] Get:175 http://mirror.einval.org/debian sid/main armhf libboost-system1.62.0 armhf 1.62.0+dfsg-10 [32.7 kB] Get:176 http://mirror.einval.org/debian sid/main armhf libboost-chrono1.62.0 armhf 1.62.0+dfsg-10 [32.9 kB] Get:177 http://mirror.einval.org/debian sid/main armhf libboost-chrono1.62-dev armhf 1.62.0+dfsg-10 [32.3 kB] Get:178 http://mirror.einval.org/debian sid/main armhf libboost-date-time1.62.0 armhf 1.62.0+dfsg-10 [41.5 kB] Get:179 http://mirror.einval.org/debian sid/main armhf libboost-serialization1.62.0 armhf 1.62.0+dfsg-10 [111 kB] Get:180 http://mirror.einval.org/debian sid/main armhf libboost-serialization1.62-dev armhf 1.62.0+dfsg-10 [179 kB] Get:181 http://mirror.einval.org/debian sid/main armhf libboost-date-time1.62-dev armhf 1.62.0+dfsg-10 [52.4 kB] Get:182 http://mirror.einval.org/debian sid/main armhf libboost-dev armhf 1.62.0.1 [3632 B] Get:183 http://mirror.einval.org/debian sid/main armhf libboost-python1.62.0 armhf 1.62.0+dfsg-10 [119 kB] Get:184 http://mirror.einval.org/debian sid/main armhf libpython2.7 armhf 2.7.15-4 [890 kB] Get:185 http://mirror.einval.org/debian sid/main armhf libexpat1-dev armhf 2.2.6-1 [125 kB] Get:186 http://mirror.einval.org/debian sid/main armhf libpython2.7-dev armhf 2.7.15-4 [30.9 MB] Get:187 http://mirror.einval.org/debian sid/main armhf libpython2-dev armhf 2.7.15-3 [20.8 kB] Get:188 http://mirror.einval.org/debian sid/main armhf libpython-dev armhf 2.7.15-3 [20.8 kB] Get:189 http://mirror.einval.org/debian sid/main armhf python2.7-dev armhf 2.7.15-4 [302 kB] Get:190 http://mirror.einval.org/debian sid/main armhf python2-dev armhf 2.7.15-3 [1216 B] Get:191 http://mirror.einval.org/debian sid/main armhf python-dev armhf 2.7.15-3 [1192 B] Get:192 http://mirror.einval.org/debian sid/main armhf libpython3.6 armhf 3.6.7~rc2-1 [1211 kB] Get:193 http://mirror.einval.org/debian sid/main armhf libpython3.6-dev armhf 3.6.7~rc2-1 [43.7 MB] Get:194 http://mirror.einval.org/debian sid/main armhf libpython3-dev armhf 3.6.6-1 [19.9 kB] Get:195 http://mirror.einval.org/debian sid/main armhf python3.6-dev armhf 3.6.7~rc2-1 [521 kB] Get:196 http://mirror.einval.org/debian sid/main armhf python3-dev armhf 3.6.6-1 [1264 B] Get:197 http://mirror.einval.org/debian sid/main armhf libboost-python1.62-dev armhf 1.62.0+dfsg-10 [167 kB] Get:198 http://mirror.einval.org/debian sid/main armhf libboost-python-dev armhf 1.62.0.1 [3802 B] Get:199 http://mirror.einval.org/debian sid/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-10 [239 kB] Get:200 http://mirror.einval.org/debian sid/main armhf libglib2.0-data all 2.58.1-2 [1105 kB] Get:201 http://mirror.einval.org/debian sid/main armhf libglib2.0-bin armhf 2.58.1-2 [115 kB] Get:202 http://mirror.einval.org/debian sid/main armhf libglib2.0-dev-bin armhf 2.58.1-2 [151 kB] Get:203 http://mirror.einval.org/debian sid/main armhf libpcre16-3 armhf 2:8.39-11 [238 kB] Get:204 http://mirror.einval.org/debian sid/main armhf libpcre32-3 armhf 2:8.39-11 [231 kB] Get:205 http://mirror.einval.org/debian sid/main armhf libpcrecpp0v5 armhf 2:8.39-11 [150 kB] Get:206 http://mirror.einval.org/debian sid/main armhf libpcre3-dev armhf 2:8.39-11 [585 kB] Get:207 http://mirror.einval.org/debian sid/main armhf pkg-config armhf 0.29-4+b1 [60.6 kB] Get:208 http://mirror.einval.org/debian sid/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get:209 http://mirror.einval.org/debian sid/main armhf libglib2.0-dev armhf 2.58.1-2 [1353 kB] Get:210 http://mirror.einval.org/debian sid/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB] Get:211 http://mirror.einval.org/debian sid/main armhf libharfbuzz-dev armhf 1.9.0-1 [965 kB] Get:212 http://mirror.einval.org/debian sid/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB] Get:213 http://mirror.einval.org/debian sid/main armhf libicu-dev armhf 60.2-6 [8727 kB] Get:214 http://mirror.einval.org/debian sid/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-10 [338 kB] Get:215 http://mirror.einval.org/debian sid/main armhf libboost-regex-dev armhf 1.62.0.1 [3674 B] Get:216 http://mirror.einval.org/debian sid/main armhf libboost-system1.62-dev armhf 1.62.0+dfsg-10 [35.1 kB] Get:217 http://mirror.einval.org/debian sid/main armhf libboost-system-dev armhf 1.62.0.1 [3554 B] Get:218 http://mirror.einval.org/debian sid/main armhf libboost-thread1.62.0 armhf 1.62.0+dfsg-10 [65.3 kB] Get:219 http://mirror.einval.org/debian sid/main armhf libboost-thread1.62-dev armhf 1.62.0+dfsg-10 [73.2 kB] Get:220 http://mirror.einval.org/debian sid/main armhf libboost-thread-dev armhf 1.62.0.1 [3440 B] Get:221 http://mirror.einval.org/debian sid/main armhf libjs-jquery all 3.2.1-1 [154 kB] Get:222 http://mirror.einval.org/debian sid/main armhf libjs-underscore all 1.8.3~dfsg-1 [63.8 kB] Get:223 http://mirror.einval.org/debian sid/main armhf libjs-sphinxdoc all 1.7.9-1 [92.3 kB] Get:224 http://mirror.einval.org/debian sid/main armhf liblapack3 armhf 3.8.0-1+b1 [1631 kB] Get:225 http://mirror.einval.org/debian sid/main armhf liblua5.1-0 armhf 5.1.5-8.1+b2 [86.8 kB] Get:226 http://mirror.einval.org/debian sid/main armhf libsqlite3-dev armhf 3.25.2-1 [710 kB] Get:227 http://mirror.einval.org/debian sid/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get:228 http://mirror.einval.org/debian sid/main armhf libwebpdemux2 armhf 0.6.1-2 [86.6 kB] Get:229 http://mirror.einval.org/debian sid/main armhf libwebpmux3 armhf 0.6.1-2 [94.1 kB] Get:230 http://mirror.einval.org/debian sid/main armhf libyaml-0-2 armhf 0.2.1-1 [40.6 kB] Get:231 http://mirror.einval.org/debian sid/main armhf pandoc-data all 2.2.1-2 [329 kB] Get:232 http://mirror.einval.org/debian sid/main armhf pandoc armhf 2.2.1-2+b1 [17.6 MB] Get:233 http://mirror.einval.org/debian sid/main armhf preview-latex-style all 11.91-1 [201 kB] Get:234 http://mirror.einval.org/debian sid/main armhf python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get:235 http://mirror.einval.org/debian sid/main armhf python-six all 1.11.0-2 [15.1 kB] Get:236 http://mirror.einval.org/debian sid/main armhf python-dateutil all 2.7.3-1 [76.6 kB] Get:237 http://mirror.einval.org/debian sid/main armhf python-epydoc all 3.0.1+dfsg-20 [221 kB] Get:238 http://mirror.einval.org/debian sid/main armhf python-numpy armhf 1:1.14.5-1+b1 [1810 kB] Get:239 http://mirror.einval.org/debian sid/main armhf python-tz all 2018.5-1 [33.5 kB] Get:240 http://mirror.einval.org/debian sid/main armhf python-pandas-lib armhf 0.23.3-1 [3121 kB] Get:241 http://mirror.einval.org/debian sid/main armhf python-pkg-resources all 40.4.3-1 [180 kB] Get:242 http://mirror.einval.org/debian sid/main armhf python-pandas all 0.23.3-1 [1743 kB] Get:243 http://mirror.einval.org/debian sid/main armhf python-pil armhf 5.3.0-1 [363 kB] Get:244 http://mirror.einval.org/debian sid/main armhf python3-alabaster all 0.7.8-1 [18.4 kB] Get:245 http://mirror.einval.org/debian sid/main armhf python3-pkg-resources all 40.4.3-1 [150 kB] Get:246 http://mirror.einval.org/debian sid/main armhf python3-tz all 2018.5-1 [26.9 kB] Get:247 http://mirror.einval.org/debian sid/main armhf python3-babel all 2.6.0+dfsg.1-1 [96.7 kB] Get:248 http://mirror.einval.org/debian sid/main armhf python3-certifi all 2018.8.24-1 [140 kB] Get:249 http://mirror.einval.org/debian sid/main armhf python3-chardet all 3.0.4-1 [80.2 kB] Get:250 http://mirror.einval.org/debian sid/main armhf python3-commonmark-bkrs all 0.5.4+ds-1 [27.7 kB] Get:251 http://mirror.einval.org/debian sid/main armhf python3-roman all 2.0.0-3 [8768 B] Get:252 http://mirror.einval.org/debian sid/main armhf python3-docutils all 0.14+dfsg-3 [377 kB] Get:253 http://mirror.einval.org/debian sid/main armhf python3-idna all 2.6-1 [34.3 kB] Get:254 http://mirror.einval.org/debian sid/main armhf python3-imagesize all 1.0.0-1 [4960 B] Get:255 http://mirror.einval.org/debian sid/main armhf python3-markupsafe armhf 1.0-1+b2 [14.1 kB] Get:256 http://mirror.einval.org/debian sid/main armhf python3-jinja2 all 2.10-1 [106 kB] Get:257 http://mirror.einval.org/debian sid/main armhf python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get:258 http://mirror.einval.org/debian sid/main armhf python3-six all 1.11.0-2 [15.2 kB] Get:259 http://mirror.einval.org/debian sid/main armhf python3-packaging all 18.0-1 [20.3 kB] Get:260 http://mirror.einval.org/debian sid/main armhf python3-pygments all 2.2.0+dfsg-2 [588 kB] Get:261 http://mirror.einval.org/debian sid/main armhf python3-recommonmark all 0.4.0+ds-2 [10.1 kB] Get:262 http://mirror.einval.org/debian sid/main armhf python3-urllib3 all 1.22-1 [97.9 kB] Get:263 http://mirror.einval.org/debian sid/main armhf python3-requests all 2.18.4-2 [77.1 kB] Get:264 http://mirror.einval.org/debian sid/main armhf sphinx-common all 1.7.9-1 [437 kB] Get:265 http://mirror.einval.org/debian sid/main armhf python3-sphinx all 1.7.9-1 [449 kB] Get:266 http://mirror.einval.org/debian sid/main armhf texlive-fonts-recommended all 2018.20181009-1 [5293 kB] Get:267 http://mirror.einval.org/debian sid/main armhf texlive-plain-generic all 2018.20181009-1 [24.1 MB] Get:268 http://mirror.einval.org/debian sid/main armhf texlive-generic-extra all 2018.20181009-1 [31.6 kB] Get:269 http://mirror.einval.org/debian sid/main armhf texlive-latex-recommended all 2018.20181009-1 [15.3 MB] Get:270 http://mirror.einval.org/debian sid/main armhf texlive-pictures all 2018.20181009-1 [4133 kB] Get:271 http://mirror.einval.org/debian sid/main armhf texlive-latex-extra all 2018.20181009-1 [12.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 314 MB in 7s (47.4 MB/s) Selecting previously unselected package libbsd0:armhf. 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Setting up libpcre16-3:armhf (2:8.39-11) ... Setting up libboost-dev:armhf (1.62.0.1) ... Setting up bison (2:3.0.4.dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up xml-core (0.18) ... Setting up libkeyutils1:armhf (1.5.9-9.3) ... 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 x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libzzip-0-13:armhf (0.13.62-3.1) ... Setting up xdg-utils (1.1.3-1) ... Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 133 added, 0 removed; done. Setting up libglib2.0-bin (2.58.1-2) ... Setting up libgfortran5:armhf (8.2.0-8) ... Setting up libgraphite2-dev:armhf (1.3.12-1) ... Setting up libncurses6:armhf (6.1+20181013-1) ... Setting up libtexluajit2:armhf (2018.20180907.48586-2) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libpython2.7-stdlib:armhf (2.7.15-4) ... Setting up libxau6:armhf (1:1.0.8-1+b2) ... Setting up autopoint (0.19.8.1-8) ... Setting up libidn11:armhf (1.33-2.2) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libdbus-1-3:armhf (1.12.10-1) ... Setting up libboost-system1.62.0:armhf (1.62.0+dfsg-10) ... Setting up liblzo2-2:armhf (2.10-0.1) ... Setting up fonts-lmodern (2.004.5-5) ... Setting up libavahi-common-data:armhf (0.7-4+b1) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up libfile-stripnondeterminism-perl (0.043-2) ... Setting up libjsoncpp1:armhf (1.7.4-3) ... Setting up libedit2:armhf (3.1-20180525-1) ... Setting up libboost-atomic1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libpython3.6-stdlib:armhf (3.6.7~rc2-1) ... Setting up libboost-date-time1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libpcre3-dev:armhf (2:8.39-11) ... Setting up python3.6 (3.6.7~rc2-1) ... Setting up pandoc (2.2.1-2+b1) ... Setting up libllvm6.0:armhf (1:6.0.1-9.1) ... Setting up flex (2.6.4-6.2) ... Setting up libsqlite3-dev:armhf (3.25.2-1) ... Setting up libboost-thread1.62.0:armhf (1.62.0+dfsg-10) ... Setting up python2.7 (2.7.15-4) ... Setting up libclang1-6.0:armhf (1:6.0.1-9.1) ... Setting up libharfbuzz0b:armhf (1.9.0-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libkrb5support0:armhf (1.16.1-1) ... Setting up ucf (3.0038) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libblas3:armhf (3.8.0-1+b1) ... 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 libboost-system1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libwebpmux3:armhf (0.6.1-2) ... Setting up libpython2.7:armhf (2.7.15-4) ... Setting up automake (1:1.16.1-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:armhf (2:1.0.9-2) ... Setting up libwebpdemux2:armhf (0.6.1-2) ... Setting up man-db (2.8.4-2+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:armhf (2.7.15-3) ... Setting up libpython2.7-dev:armhf (2.7.15-4) ... Setting up libavahi-common3:armhf (0.7-4+b1) ... Setting up python2.7-dev (2.7.15-4) ... Setting up libxcb1:armhf (1.13.1-1) ... Setting up libharfbuzz-gobject0:armhf (1.9.0-1) ... Setting up libboost-chrono1.62.0:armhf (1.62.0+dfsg-10) ... Setting up libpython3.6:armhf (3.6.7~rc2-1) ... Setting up libtool (2.4.6-6) ... Setting up libpaper1:armhf (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up libpython3-stdlib:armhf (3.6.6-1) ... Setting up libsm6:armhf (2:1.2.2-1+b3) ... Setting up libk5crypto3:armhf (1.16.1-1) ... Setting up libpaper-utils (1.1.24+nmu5) ... Setting up fontconfig-config (2.13.1-1) ... Setting up libxcb-render0:armhf (1.13.1-1) ... Setting up tex-common (6.10) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python3 (3.6.6-1) ... Setting up libboost-system-dev:armhf (1.62.0.1) ... Setting up python3-alabaster (0.7.8-1) ... Setting up liblapack3:armhf (3.8.0-1+b1) ... 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 python3-idna (2.6-1) ... Setting up python3-six (1.11.0-2) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up doxygen (1.8.13-10) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-certifi (2018.8.24-1) ... Setting up python3-commonmark-bkrs (0.5.4+ds-1) ... Setting up preview-latex-style (11.91-1) ... Setting up python3-pkg-resources (40.4.3-1) ... Setting up libboost-chrono1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libpython3.6-dev:armhf (3.6.7~rc2-1) ... Setting up python2 (2.7.15-3) ... Setting up python3-markupsafe (1.0-1+b2) ... Setting up libpython2-dev:armhf (2.7.15-3) ... Setting up libpython-stdlib:armhf (2.7.15-3) ... Setting up gir1.2-harfbuzz-0.0:armhf (1.9.0-1) ... Setting up python3-chardet (3.0.4-1) ... Setting up python3-jinja2 (2.10-1) ... Setting up python2-dev (2.7.15-3) ... Setting up libboost-thread1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libxcb-shm0:armhf (1.13.1-1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libavahi-client3:armhf (0.7-4+b1) ... Setting up python3-urllib3 (1.22-1) ... Setting up libkrb5-3:armhf (1.16.1-1) ... Setting up python3-packaging (18.0-1) ... Setting up python3.6-dev (3.6.7~rc2-1) ... Setting up python3-lib2to3 (3.6.6-1) ... Setting up python3-tz (2018.5-1) ... Setting up python3-distutils (3.6.6-1) ... Setting up python (2.7.15-3) ... Setting up libpython3-dev:armhf (3.6.6-1) ... Setting up python3-pygments (2.2.0+dfsg-2) ... Setting up libpython-dev:armhf (2.7.15-3) ... Setting up libfontconfig1:armhf (2.13.1-1) ... Setting up python3-roman (2.0.0-3) ... Setting up python3-imagesize (1.0.0-1) ... Setting up libboost-thread-dev:armhf (1.62.0.1) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up libglib2.0-dev-bin (2.58.1-2) ... Setting up python-dev (2.7.15-3) ... Setting up python-tz (2018.5-1) ... Setting up python-pkg-resources (40.4.3-1) ... Setting up libglib2.0-dev:armhf (2.58.1-2) ... Setting up python-numpy (1:1.14.5-1+b1) ... Setting up libxmu6:armhf (2:1.1.2-2) ... 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 libgssapi-krb5-2:armhf (1.16.1-1) ... Setting up python-epydoc (3.0.1+dfsg-20) ... Setting up python-six (1.11.0-2) ... Setting up python-pandas-lib (0.23.3-1) ... Setting up python3-requests (2.18.4-2) ... Setting up dh-python (3.20180927) ... Setting up python-pil:armhf (5.3.0-1) ... Setting up libcups2:armhf (2.2.8-5) ... Setting up libxi6:armhf (2:1.7.9-1) ... Setting up libxaw7:armhf (2:1.0.13-1+b2) ... Setting up libcairo2:armhf (1.16.0-1) ... Setting up libsasl2-modules-db:armhf (2.1.27~rc8-1) ... Setting up libsasl2-2:armhf (2.1.27~rc8-1) ... Setting up python3-dev (3.6.6-1) ... Setting up python-dateutil (2.7.3-1) ... Setting up libcupsimage2:armhf (2.2.8-5) ... Setting up libldap-2.4-2:armhf (2.4.46+dfsg-5) ... Setting up libgs9:armhf (9.25~dfsg-4) ... Setting up libboost-python1.62-dev (1.62.0+dfsg-10) ... Setting up libcurl4:armhf (7.61.0-1) ... Setting up python-pandas (0.23.3-1) ... Setting up libboost-python-dev (1.62.0.1) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-3) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-3) ... 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-2) ... Setting up python3-sphinx (1.7.9-1) ... 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 Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ... Setting up libicu60:armhf (60.2-6) ... Setting up libharfbuzz-icu0:armhf (1.9.0-1) ... Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-10) ... Setting up texlive-binaries (2018.20180907.48586-2) ... 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 libxml2:armhf (2.9.4+dfsg1-7+b1) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up texlive-base (2018.20181009-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up icu-devtools (60.2-6) ... Setting up texlive-fonts-recommended (2018.20181009-1) ... Setting up texlive-plain-generic (2018.20181009-1) ... Setting up texlive-latex-base (2018.20181009-1) ... Setting up texlive-latex-recommended (2018.20181009-1) ... Setting up gettext (0.19.8.1-8) ... Setting up libarchive13:armhf (3.2.2-5) ... Setting up texlive-pictures (2018.20181009-1) ... Setting up libicu-dev (60.2-6) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up texlive-generic-extra (2018.20181009-1) ... Setting up latexmk (1:4.60-0.1) ... Setting up cmake (3.12.3-2) ... Setting up libharfbuzz-dev:armhf (1.9.0-1) ... Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ... Setting up texlive-latex-extra (2018.20181009-1) ... Setting up po-debconf (1.0.20) ... Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-10) ... Setting up libboost-regex-dev:armhf (1.62.0.1) ... Setting up debhelper (11.4.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.043-2) ... Setting up sbuild-build-depends-rdkit-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-6) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.10) ... 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. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-arm64 arm64 (aarch64) Toolchain package versions: binutils_2.31.1-7 dpkg-dev_1.19.2 g++-8_8.2.0-8 gcc-8_8.2.0-8 libc6-dev_2.27-6 libstdc++-8-dev_8.2.0-8 libstdc++6_8.2.0-8 linux-libc-dev_4.18.10-2 Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-7 binutils-arm-linux-gnueabihf_2.31.1-7 binutils-common_2.31.1-7 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2+b1 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20180409 cmake_3.12.3-2 cmake-data_3.12.3-2 coreutils_8.30-1 cpp_4:8.2.0-1 cpp-8_8.2.0-8 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.4.1 debian-archive-keyring_2017.7 debianutils_4.8.6 dh-autoreconf_19 dh-python_3.20180927 dh-strip-nondeterminism_0.043-2 diffutils_1:3.6-1 docutils-common_0.14+dfsg-3 doxygen_1.8.13-10 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-2 e2fsprogs_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20180808-2 flex_2.6.4-6.2 fontconfig-config_2.13.1-1 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-5 g++_4:8.2.0-1 g++-8_8.2.0-8 gcc_4:8.2.0-1 gcc-8_8.2.0-8 gcc-8-base_8.2.0-8 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gir1.2-glib-2.0_1.58.0-1 gir1.2-harfbuzz-0.0_1.9.0-1 gpgv_2.2.10-3 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 icu-devtools_60.2-6 init-system-helpers_1.54 intltool-debian_0.35.0+20060710.4 latexmk_1:4.60-0.1 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libarchive13_3.2.2-5 libasan5_8.2.0-8 libatomic1_8.2.0-8 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libavahi-client3_0.7-4+b1 libavahi-common-data_0.7-4+b1 libavahi-common3_0.7-4+b1 libbinutils_2.31.1-7 libbison-dev_2:3.0.4.dfsg-1+b1 libblas3_3.8.0-1+b1 libblkid1_2.32.1-0.1 libboost-atomic1.62-dev_1.62.0+dfsg-10 libboost-atomic1.62.0_1.62.0+dfsg-10 libboost-chrono1.62-dev_1.62.0+dfsg-10 libboost-chrono1.62.0_1.62.0+dfsg-10 libboost-date-time1.62-dev_1.62.0+dfsg-10 libboost-date-time1.62.0_1.62.0+dfsg-10 libboost-dev_1.62.0.1 libboost-python-dev_1.62.0.1 libboost-python1.62-dev_1.62.0+dfsg-10 libboost-python1.62.0_1.62.0+dfsg-10 libboost-regex-dev_1.62.0.1 libboost-regex1.62-dev_1.62.0+dfsg-10 libboost-regex1.62.0_1.62.0+dfsg-10 libboost-serialization1.62-dev_1.62.0+dfsg-10 libboost-serialization1.62.0_1.62.0+dfsg-10 libboost-system-dev_1.62.0.1 libboost-system1.62-dev_1.62.0+dfsg-10 libboost-system1.62.0_1.62.0+dfsg-10 libboost-thread-dev_1.62.0.1 libboost-thread1.62-dev_1.62.0+dfsg-10 libboost-thread1.62.0_1.62.0+dfsg-10 libboost1.62-dev_1.62.0+dfsg-10 libbrotli1_1.0.6-1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-6 libc-dev-bin_2.27-6 libc6_2.27-6 libc6-dev_2.27-6 libcairo2_1.16.0-1 libcap-ng0_0.7.9-1 libcc1-0_8.2.0-8 libclang1-6.0_1:6.0.1-9.1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcups2_2.2.8-5 libcupsimage2_2.2.8-5 libcurl4_7.61.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdpkg-perl_1.19.2 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-2 libfontconfig1_2.13.1-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-8 libgcc1_1:8.2.0-8 libgcrypt20_1.8.3-1 libgdbm-compat4_1.18-2 libgdbm5_1.14.1-6+b1 libgdbm6_1.18-2 libgfortran5_8.2.0-8 libgirepository-1.0-1_1.58.0-1 libglib2.0-0_2.58.1-2 libglib2.0-bin_2.58.1-2 libglib2.0-data_2.58.1-2 libglib2.0-dev_2.58.1-2 libglib2.0-dev-bin_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-8 libgpg-error0_1.32-3 libgraphite2-3_1.3.12-1 libgraphite2-dev_1.3.12-1 libgs9_9.25~dfsg-4 libgs9-common_9.25~dfsg-4 libgssapi-krb5-2_1.16.1-1 libharfbuzz-dev_1.9.0-1 libharfbuzz-gobject0_1.9.0-1 libharfbuzz-icu0_1.9.0-1 libharfbuzz0b_1.9.0-1 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libijs-0.35_0.35-13 libisl19_0.20-2 libjbig0_2.1-3.1+b2 libjbig2dec0_0.15-1 libjpeg62-turbo_1:1.5.2-2+b1 libjs-jquery_3.2.1-1 libjs-sphinxdoc_1.7.9-1 libjs-underscore_1.8.3~dfsg-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libkpathsea6_2018.20180907.48586-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 liblapack3_3.8.0-1+b1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.46+dfsg-5 libldap-common_2.4.46+dfsg-5 libllvm6.0_1:6.0.1-9.1 liblua5.1-0_5.1.5-8.1+b2 liblz4-1_1.8.2-1 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4-1 libnghttp2-14_1.34.0-1 libopenjp2-7_2.3.0-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam0g_1.1.8-3.8 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-11 libpcre3_2:8.39-11 libpcre3-dev_2:8.39-11 libpcre32-3_2:8.39-11 libpcrecpp0v5_2:8.39-11 libperl5.26_5.26.2-7+b1 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libpng16-16_1.6.34-2 libpotrace0_1.15-1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libptexenc1_2018.20180907.48586-2 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-4 libpython2.7-dev_2.7.15-4 libpython2.7-minimal_2.7.15-4 libpython2.7-stdlib_2.7.15-4 libpython3-dev_3.6.6-1 libpython3-stdlib_3.6.6-1 libpython3.6_3.6.7~rc2-1 libpython3.6-dev_3.6.7~rc2-1 libpython3.6-minimal_3.6.7~rc2-1 libpython3.6-stdlib_3.6.7~rc2-1 libreadline7_7.0-5 librhash0_1.3.6-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libsqlite3-dev_3.25.2-1 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.1-1 libstdc++-8-dev_8.2.0-8 libstdc++6_8.2.0-8 libsynctex2_2018.20180907.48586-2 libsystemd0_239-10 libtasn1-6_4.13-3 libtexlua52_2018.20180907.48586-2 libtexlua53_2018.20180907.48586-2 libtexluajit2_2018.20180907.48586-2 libtiff5_4.0.9-6 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-8 libudev1_239-10 libunistring2_0.9.10-1 libuuid1_2.32.1-0.1 libuv1_1.23.1-1 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libwoff1_1.0.2-1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxapian30_1.4.7-4 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.13.1-1 libxcb-shm0_1.13.1-1 libxcb1_1.13.1-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-7+b1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libxxhash0_0.6.5-1 libyaml-0-2_0.2.1-1 libzstd1_1.3.5+dfsg-1 libzzip-0-13_0.13.62-3.1 linux-libc-dev_4.18.10-2 login_1:4.5-1.1 lsb-base_9.20170808 m4_1.4.18-1 make_4.2.1-1.2 man-db_2.8.4-2+b1 mawk_1.3.3-17+b3 mime-support_3.61 mount_2.32.1-0.1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 openssl_1.1.1-1 pandoc_2.2.1-2+b1 pandoc-data_2.2.1-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7+b1 perl-base_5.26.2-7+b1 perl-modules-5.26_5.26.2-7 pkg-config_0.29-4+b1 po-debconf_1.0.20 poppler-data_0.4.9-2 preview-latex-style_11.91-1 procps_2:3.3.15-2 python_2.7.15-3 python-babel-localedata_2.6.0+dfsg.1-1 python-dateutil_2.7.3-1 python-dev_2.7.15-3 python-epydoc_3.0.1+dfsg-20 python-minimal_2.7.15-3 python-numpy_1:1.14.5-1+b1 python-pandas_0.23.3-1 python-pandas-lib_0.23.3-1 python-pil_5.3.0-1 python-pkg-resources_40.4.3-1 python-six_1.11.0-2 python-tz_2018.5-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-4 python2.7-dev_2.7.15-4 python2.7-minimal_2.7.15-4 python3_3.6.6-1 python3-alabaster_0.7.8-1 python3-babel_2.6.0+dfsg.1-1 python3-certifi_2018.8.24-1 python3-chardet_3.0.4-1 python3-commonmark-bkrs_0.5.4+ds-1 python3-dev_3.6.6-1 python3-distutils_3.6.6-1 python3-docutils_0.14+dfsg-3 python3-idna_2.6-1 python3-imagesize_1.0.0-1 python3-jinja2_2.10-1 python3-lib2to3_3.6.6-1 python3-markupsafe_1.0-1+b2 python3-minimal_3.6.6-1 python3-packaging_18.0-1 python3-pkg-resources_40.4.3-1 python3-pygments_2.2.0+dfsg-2 python3-pyparsing_2.2.0+dfsg1-2 python3-recommonmark_0.4.0+ds-2 python3-requests_2.18.4-2 python3-roman_2.0.0-3 python3-six_1.11.0-2 python3-sphinx_1.7.9-1 python3-tz_2018.5-1 python3-urllib3_1.22-1 python3.6_3.6.7~rc2-1 python3.6-dev_3.6.7~rc2-1 python3.6-minimal_3.6.7~rc2-1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rdkit-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 sgml-base_1.29 sphinx-common_1.7.9-1 sysvinit-utils_2.88dsf-59.11 t1utils_1.41-2 tar_1.30+dfsg-2 tex-common_6.10 texlive-base_2018.20181009-1 texlive-binaries_2018.20180907.48586-2 texlive-fonts-recommended_2018.20181009-1 texlive-generic-extra_2018.20181009-1 texlive-latex-base_2018.20181009-1 texlive-latex-extra_2018.20181009-1 texlive-latex-recommended_2018.20181009-1 texlive-pictures_2018.20181009-1 texlive-plain-generic_2018.20181009-1 tzdata_2018f-1 ucf_3.0038 util-linux_2.32.1-0.1 x11-common_1:7.7+19 xdg-utils_1.1.3-1 xml-core_0.18 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Mar 26 11:41:35 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rdkit_201709.3+dfsg-1.dsc dpkg-source: info: extracting rdkit in /<>/rdkit-201709.3+dfsg dpkg-source: info: unpacking rdkit_201709.3+dfsg.orig.tar.xz dpkg-source: info: unpacking rdkit_201709.3+dfsg-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=POSIX LC_COLLATE=C LC_CTYPE=en_GB.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=sid-armhf-sbuild SCHROOT_CHROOT_NAME=sid-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-armhf-sbuild-41abf9f1-612a-4bfc-9398-04d81a39e514 SCHROOT_UID=108 SCHROOT_USER=sbuild SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 201709.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python2 --buildsystem=cmake --parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rdkit-201709.3+dfsg' find /<>/rdkit-201709.3+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 dh_auto_clean make[1]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+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 8.2.0 -- The CXX compiler identification is GNU 8.2.0 -- 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 PythonInterp: /usr/bin/python (found version "2.7.15") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython2.7.so (found version "2.7.15+") -- Boost version: 1.62.0 -- Found the following Boost libraries: -- python Python Install directory /usr/lib/python2.7/dist-packages -- 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: 1.62.0 -- Found the following Boost libraries: -- thread -- system -- chrono -- date_time -- atomic -- Boost version: 1.62.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition == Updating Filters.cpp from pains file == Done updating pains files -- Boost version: 1.62.0 -- Found the following Boost libraries: -- regex -- 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: /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>/rdkit-201709.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rdkit-201709.3+dfsg' dh_auto_build cd obj-arm-linux-gnueabihf && make -j4 make[2]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -H/<>/rdkit-201709.3+dfsg -B/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/External/INCHI-API /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target inchi_support Scanning dependencies of target hc make[4]: Leaving directory '/<>/rdkit-201709.3+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]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API && /usr/bin/cmake -E copy /<>/rdkit-201709.3+dfsg/External/INCHI-API/python/noinchi.py /<>/rdkit-201709.3+dfsg/rdkit/Chem/inchi.py make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target RDGeneral Scanning dependencies of target ChemicalFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/hc.dir/hc.c.o -c /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh/hc.c [ 0%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DChemicalFeatures_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/FreeChemicalFeature.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.cpp [ 0%] Built target inchi_support [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.cpp [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/hc.dir/hcdriver.c.o -c /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh/hcdriver.c [ 0%] Linking C shared library ../../../../lib/libRDKithc.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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.1.2017.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2017.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 0%] Built target hc [ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/Dict.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/LocaleSwitcher.cpp /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2017.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2017.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] Built target ChemicalFeatures [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/versions.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2017.09.3 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 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] 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 -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/RDBoost /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target RDBoost make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build Scanning dependencies of target testRDValue Scanning dependencies of target testDict make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target DataStructs make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DRDBoost_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDict.dir/testDict.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testDict.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVect.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/SparseBitVect.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h:39, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h:38, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp: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 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 [ 2%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2017.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization -lpthread -lboost_thread -lboost_system In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h:39, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h:38, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp:1: /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); ^~~~~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2017.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testDict.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>:: ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] Built target RDBoost make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= Scanning dependencies of target testMatrices make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' /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)...); ^~~~~~~~~~~~~~~~~ [ 2%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/testMatrices.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h:39, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h:38, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp: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 = {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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h:39, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h:38, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp:1: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h:39, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h:38, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/testRDValue.cpp:1: /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)...); ^~~~~~~~~~~~~~~~~ [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.cpp [ 2%] Linking CXX executable testRDValue cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] Built target testRDValue make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/EigenSolvers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= Scanning dependencies of target EigenSolvers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DEigenSolvers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Utils.cpp [ 3%] Linking CXX executable testDict cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 3%] Built target testDict make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Catalogs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= Scanning dependencies of target Catalogs make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.cpp [ 4%] Linking CXX executable testMatrices cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 4%] Built target testMatrices make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Query /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Query /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= Scanning dependencies of target testQuery make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testQuery.dir/test.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Query/test.cpp [ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o [ 5%] Built target EigenSolvers make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/base64.cpp make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= Scanning dependencies of target testMatCalc make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitOps.cpp [ 5%] Linking CXX executable testMatCalc cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target testMatCalc [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteDistMat.cpp [ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogParams.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteValueVect.cpp [ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogEntry.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2017.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Built target Catalogs make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/SimDivPickers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target SimDivPickers make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/DistPicker.cpp [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/MaxMinPicker.cpp [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Linking CXX executable testQuery cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Built target testQuery make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Scanning dependencies of target Clustering make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/FPBReader.cpp [ 7%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DClustering_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh/Clustering.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/MultiFPBReader.cpp [ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2017.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread 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 /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h:15, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2017.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] Built target SimDivPickers make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/testChemicalFeatures.cpp 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 /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h:15, from /<>/rdkit-201709.3+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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system 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 /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h:15, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h:15, from /<>/rdkit-201709.3+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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] Built target Clustering make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= /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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ Scanning dependencies of target rdBase make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap/RDBase.cpp /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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/SimDivPickers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target testSimDivPickers make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/testPickers.cpp 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 /<>/rdkit-201709.3+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, ^~~~~~~~~~~~~~~~~~~~~~~~~ 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 /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/DataStructs/MultiFPBReader.cpp:11: /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:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 [ 9%] Linking CXX executable testChemicalFeatures cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target testChemicalFeatures In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Ranking.h:20, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Ranking.h:20, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Linking CXX executable testSimDivPickers cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread ../../lib/libRDKithc.so.1.2017.09.3 make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target testSimDivPickers In file included from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap/RDBase.cpp:15: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept [ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2017.09.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 9%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= Scanning dependencies of target testMultiFPB Scanning dependencies of target testDataStructs Scanning dependencies of target testFPB make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/testMultiFPB.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/testFPB.cpp [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp: In function 'int main()': /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp:1399:12: warning: catching polymorphic type 'class IndexErrorException' by value [-Wcatch-value=] } catch (IndexErrorException) { ^~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp: In instantiation of 'void Test(T) [with T = SparseBitVect]': /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp:1418:17: required from here /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp:118:5: warning: catching polymorphic type 'class IndexErrorException' by value [-Wcatch-value=] } catch (IndexErrorException) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp: In instantiation of 'void Test(T) [with T = ExplicitBitVect]': /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp:1424:19: required from here /<>/rdkit-201709.3+dfsg/Code/DataStructs/testDatastructs.cpp:118:5: warning: catching polymorphic type 'class IndexErrorException' by value [-Wcatch-value=] [ 9%] Linking CXX executable testFPB cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target testFPB make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target cDataStructs make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/DataStructs.cpp [ 11%] Linking CXX executable testMultiFPB cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 11%] Built target testMultiFPB make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= Scanning dependencies of target RDGeometryLib make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/point.cpp /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform2D.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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_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); ^~~~~~~~~~~~~~~~~ [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/DiscreteValueVect.cpp /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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:13, 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 /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:2, from /<>/rdkit-201709.3+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: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)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Linking CXX executable testDataStructs cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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 make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 12%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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 Scanning dependencies of target rdMetricMatrixCalc make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 12%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /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 [ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform3D.cpp [ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/UniformGrid3D.cpp [ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/SparseIntVect.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'double RDDataManip::EuclideanDistanceMetric(const T1&, const T2&, unsigned int) [with T1 = PySequenceHolder; T2 = PySequenceHolder]': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 12%] Built target rdMetricMatrixCalc make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target rdSimDivPickers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp [ 13%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/GridUtils.cpp [ 13%] Linking CXX shared module ../../../rdkit/rdBase.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 13%] Built target rdBase [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Geometry/GridUtils.h:13, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Geometry/GridUtils.h:13, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 14%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target RDGeometryLib make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target InfoTheory make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/c++ -DInfoTheory_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoBitRanker.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoBitRanker.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+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]': /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:62:48: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] return python::extract(dp_obj(i, j)); ^ /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:62:48: 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoBitRanker.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 14%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2017.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2017.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target InfoTheory make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/testTransforms.cpp make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= Scanning dependencies of target testGrid make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/testGrid.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long int]': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 15%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKithc.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Built target rdSimDivPickers make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Geometry/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target rdGeometry make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/Wrap/Point.cpp /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long unsigned int]': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 15%] Linking CXX executable testGrid cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Linking CXX executable testTransforms cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 [ 15%] Built target testGrid /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/Wrap/UniformGrid3D.cpp make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Built target testTransforms make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= Scanning dependencies of target Alignment make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/AlignPoints.cpp [ 15%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2017.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Built target Alignment make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Scanning dependencies of target Optimizer make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/BFGSOpt.cpp [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 16%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/LinearSearch.cpp [ 16%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2017.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 16%] Built target Optimizer make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= Scanning dependencies of target GraphMol make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.cpp make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target rdInfoTheory make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Geometry/Wrap/rdGeometry.cpp [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 17%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 17%] Built target rdGeometry [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryAtom.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryBond.cpp [ 18%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Bond.cpp [ 18%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FindRings.cpp [ 19%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 19%] Built target rdInfoTheory make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ML/Data /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Scanning dependencies of target cQuantize make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 19%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ML/Data/cQuantize.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FindRings.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)...); ^~~~~~~~~~~~~~~~~ [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.cpp [ 20%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 20%] Built target cQuantize make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target testAlignment make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 21%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/testAlignment.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.cpp [ 22%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/wrap_FPB.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 22%] Linking CXX executable testAlignment cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread /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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 22%] Built target testAlignment make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target rdAlignment make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 22%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/Wrap/rdAlignment.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setVal(const string&, T&) [with T = std::vector >]': /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h:20, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h:20, from /<>/rdkit-201709.3+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 /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h:20, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/PeriodicTable.cpp /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h:20, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/PeriodicTable.h:14, from /<>/rdkit-201709.3+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:64, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/PeriodicTable.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/atomic_data.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void RDNumeric::Alignments::GetPointsFromPythonSequence(boost::python::api::object&, RDGeom::Point3DConstPtrVect&)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 22%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DataStructs/Wrap/wrap_Utils.cpp /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.cpp [ 23%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] Built target rdAlignment make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= Scanning dependencies of target testOptimizer make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/testOptimizer.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolPickler.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Snapshot.h:13, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/BFGSOpt.h:12, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/testOptimizer.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 = {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 /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Snapshot.h:13, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/BFGSOpt.h:12, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/testOptimizer.cpp:15: /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); ^~~~~~~~~~~~~~~~~ [ 24%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system [ 24%] Linking CXX executable testOptimizer cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 24%] Built target testOptimizer make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ForceField /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= [ 24%] Built target cDataStructs [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Canon.cpp Scanning dependencies of target ForceField make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/AtomIterators.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h:13, from /<>/rdkit-201709.3+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/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:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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:64, from /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h:13, from /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.cpp:11: /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleBend.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/BondStretch.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/BondIterators.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Aromaticity.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Kekulize.cpp [ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Nonbonded.cpp [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDiscriminators.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Aromaticity.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)...); ^~~~~~~~~~~~~~~~~ [ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Inversion.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.h:14, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ConjugHybrid.cpp [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/AddHs.cpp [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Matrices.cpp [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionAngle.cpp [ 26%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Chirality.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/DistanceConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/AddHs.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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/RingInfo.cpp [ 27%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.cpp [ 27%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Renumber.cpp [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+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:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ [ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/AdjustQuery.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Resonance.cpp [ 28%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/new_canon.cpp [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/PositionConstraint.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Params.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleBend.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.cpp /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)...); ^~~~~~~~~~~~~~~~~ [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/StretchBend.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/OopBend.cpp [ 29%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2017.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/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/new_canon.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionAngle.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 30%] Built target GraphMol make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= Scanning dependencies of target SubstructMatch make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 31%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructMatch.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Nonbonded.cpp make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= Scanning dependencies of target SmilesParse make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/DistanceConstraint.cpp [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParse.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>:: ^~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp: In function 'void SmilesParseOps::AdjustAtomChiralityFlags(RDKit::RWMol*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:320:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (selfPos->first != static_cast((*atomIt)->getIdx())) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:323:38: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] CHECK_INVARIANT(selfPos->first == static_cast((*atomIt)->getIdx()), ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:100:9: note: in definition of macro 'CHECK_INVARIANT' if (!(expr)) { \ ^~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionConstraint.cpp [ 31%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructUtils.cpp [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h:14, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/PositionConstraint.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.cpp: In function 'std::__cxx11::string RDKit::{anonymous}::getNonQueryBondSmarts(const RDKit::QueryBond*, int)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.cpp:599:63: warning: unused parameter 'atomToLeftIdx' [-Wunused-parameter] std::string getNonQueryBondSmarts(const QueryBond *qbond, int atomToLeftIdx) { ~~~~^~~~~~~~~~~~~ [ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.cpp [ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 32%] Built target SubstructMatch [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/smarts.tab.cpp /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.cpp: In constructor 'ForceFields::MMFF::MMFFAromCollection::MMFFAromCollection(const uint8_t*)': /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.cpp:50:49: warning: division 'sizeof (const uint8_t* {aka const unsigned char*}) / sizeof (const uint8_t {aka const unsigned char})' does not compute the number of array elements [-Wsizeof-pointer-div] for (unsigned int i = 0; i < sizeof(mmffArom) / sizeof(mmffArom[0]); ++i) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.cpp:46:62: note: first 'sizeof' operand was declared here MMFFAromCollection::MMFFAromCollection(const boost::uint8_t *mmffArom) { ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/smiles.tab.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:18, from /<>/rdkit-201709.3+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 smarts.yy: In function 'void yysmarts_error(const char*, std::vector*, void*, const char*)': smarts.yy:25:29: warning: unused parameter 'input' [-Wunused-parameter] smarts.yy:26:46: warning: unused parameter 'ms' [-Wunused-parameter] smarts.yy:27:9: warning: unused parameter 'scanner' [-Wunused-parameter] /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 /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 In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:18, from /<>/rdkit-201709.3+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::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::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); ^~~~~~~~~~~~~~~~~ /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::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); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ /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::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); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.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 = {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/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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from smarts.yy: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)...); ^~~~~~~~~~~~~~~~~ smiles.yy: In function 'void yysmiles_error(const char*, std::vector*, std::__cxx11::list*, void*, const char*)': smiles.yy:38:29: warning: unused parameter 'input' [-Wunused-parameter] smiles.yy:40:42: warning: unused parameter 'branchPoints' [-Wunused-parameter] smiles.yy:41:9: warning: unused parameter 'scanner' [-Wunused-parameter] [ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2017.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread 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)...); ^~~~~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2017.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target ForceField make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target MolTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DMolTransforms_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/MolTransforms.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:15: /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); ^~~~~~~~~~~~~~ [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/lex.yysmarts.cpp make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= Scanning dependencies of target Depictor make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.cpp [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/lex.yysmiles.cpp /scratch/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp: In function 'int yy_get_next_buffer(yyscan_t)': /scratch/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmarts.cpp:1906:47: warning: comparison of integer expressions of different signedness: 'int' and 'yy_size_t' {aka 'unsigned int'} [-Wsign-compare] /scratch/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmiles.cpp: In function 'int yy_get_next_buffer(yyscan_t)': /scratch/RDKit_git/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:2234:47: warning: comparison of integer expressions of different signedness: 'int' and 'yy_size_t' {aka 'unsigned int'} [-Wsign-compare] In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from smiles.ll:20: /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/stl_vector.h: In function 'unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const INT_POINT2D_MAP*, bool, bool, unsigned int, unsigned int, 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/vector.tcc: In function 'int yysmiles_lex(YYSTYPE*, yyscan_t)': /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%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 34%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/DepictUtils.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread [ 34%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 34%] Built target MolTransforms make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= Scanning dependencies of target Subgraphs make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -I/<>/rdkit-201709.3+dfsg/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/Subgraphs.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Built target SmilesParse make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target PartialCharges make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h:13, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h:13, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 35%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.cpp In file included from /usr/include/c++/8/map:60, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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, /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, /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: 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, [ 35%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -I/<>/rdkit-201709.3+dfsg/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.cpp /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, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::openAngles(const double*, 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: In constructor 'RDDepict::EmbeddedFrag::EmbeddedFrag(unsigned int, const RDKit::ROMol*)': /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+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, /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: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: 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::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, /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::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: 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 '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: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, make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp /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, /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: 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, [ 35%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2017.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Built target Depictor make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target MolChemicalFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target PartialCharges make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ShapeHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 36%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h:31, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h:13, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h:31, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h:13, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~ [ 36%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target Subgraphs [ 37%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h:13, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h:13, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 37%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2017.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2017.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] Built target ShapeHelpers make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target MolCatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] Built target rdMolTransforms [ 37%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target ReducedGraphs make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= Scanning dependencies of target Trajectory make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp [ 38%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2017.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2017.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 38%] Built target MolCatalog make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target SLNParse make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 38%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParse.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:16, from /<>/rdkit-201709.3+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 /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>:: ^~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:76:12: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 s) - d_snapshotVect->begin()); ^ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: 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/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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:16, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: /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/vector.tcc: In function 'RDKit::ROMol* RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const RDKit::ROMol&, std::vector >*)': /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)...); ^~~~~~~~~~~~~~~~~ [ 38%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2017.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2017.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 38%] Built target Trajectory make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= Scanning dependencies of target rdqueries make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 39%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/rdqueries.cpp [ 39%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2017.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2017.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 39%] Built target ReducedGraphs make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemicalFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 39%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2017.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2017.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 40%] Built target MolChemicalFeatures [ 40%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParse.cpp:36: /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)...); ^~~~~~~~~~~~~~~~~ make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ForceFieldHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp [ 41%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 41%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Queries.cpp [ 41%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 41%] Built target rdChemicalFeatures [ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp [ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h:38, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryAtom.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitQueries.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Queries.cpp:16: /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*; T = double]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery >::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:723:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:729:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:731:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*; T = bool]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*; T = int]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*; T = double]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery >::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:723:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:729:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:731:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*; T = bool]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*; T = int]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ [ 41%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/sln.tab.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp: In member function 'void RDKit::MMFF::MMFFMolProperties::setMMFFHydrogenType(const RDKit::Atom*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp:2343:13: warning: this statement may fall through [-Wimplicit-fallthrough=] if (isHOS) { ^~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp:2350:11: note: here default: ^~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ 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] [ 41%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/lex.yysln.cpp 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)...); ^~~~~~~~~~~~~~~~~ /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] [ 41%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 41%] Built target rdqueries make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= Scanning dependencies of target FileParsers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 42%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp [ 42%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2017.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2017.09.3 -lboost_regex ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2017.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 42%] Built target SLNParse make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target MolAlign make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 43%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/AlignMolecules.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp: In function 'RDKit::Bond* RDKit::{anonymous}::ParseMolFileBondLine(const string&, unsigned int)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:1355:21: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] } catch (boost::bad_lexical_cast) { ^~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:1383:21: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] } catch (boost::bad_lexical_cast) { ^~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:1391:21: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] } catch (boost::bad_lexical_cast) { ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+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:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Vector.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Matrix.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/SquareMatrix.h:13, from /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform3D.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h:13, from /<>/rdkit-201709.3+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:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+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: 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)...); ^~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+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)': /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); ^~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.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/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.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 /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.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)...); ^~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h:13, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ 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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:13: /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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.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 = {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>:: ^~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'ForceFields::CrystalFF::ExpTorsionAngleCollection::ExpTorsionAngleCollection(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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp: In function 'std::__cxx11::string RDKit::MolToMolBlock(const RDKit::ROMol&, bool, int, bool, bool)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:1193:12: warning: catching polymorphic type 'class RDKit::{anonymous}::RequiresV3000Exception' by value [-Wcatch-value=] } catch (RequiresV3000Exception) { ^~~~~~~~~~~~~~~~~~~~~~ [ 43%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2017.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 43%] Built target MolAlign make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolqueryTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/querytest.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 44%] Built target ForceFieldHelpers make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolcpTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/cptest.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.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 = {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:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryAtom.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitQueries.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/querytest.cpp:13: /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*; T = double]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ForwardSDMolSupplier.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>:: ^~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*; T = double]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery >::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:723:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:729:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:731:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Bond*; T = int]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery >::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:723:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:729:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:731:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*; T = int]': /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:659:16: required from here /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:665:9: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException e) { ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:667:9: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] } catch (boost::bad_any_cast) { ^~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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 /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)...); ^~~~~~~~~~~~~~~~~ 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:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestCanon make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:14: /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); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/testCanon.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/querytest.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:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/cptest.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>:: ^~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SDMolSupplier.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/cptest.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); ^~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/testCanon.cpp: In function 'int main(int, char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/testCanon.cpp:180:18: warning: catching polymorphic type 'class RDKit::MolSanitizeException' by value [-Wcatch-value=] } catch (MolSanitizeException) { ^~~~~~~~~~~~~~~~~~~~ [ 45%] Linking CXX executable graphmolcpTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 45%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMemTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/memtest1.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/testCanon.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 function 'void permuteAtoms(RDKit::RWMol*)': /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 45%] Linking CXX executable graphmoltestCanon In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -o graphmoltestCanon ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 45%] Built target graphmoltestCanon make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolIterTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/itertest.cpp /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); ^~~~~~~~~~~~~~~~~ [ 46%] Linking CXX executable graphmolqueryTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Built target graphmolqueryTest [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SDWriter.cpp make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target ChemTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/memtest1.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)...); ^~~~~~~~~~~~~~~~~ [ 46%] Linking CXX executable graphmolMemTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Built target graphmolMemTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smaTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/smatest.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 46%] Linking CXX executable graphmolIterTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Built target graphmolIterTest make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FilterCatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 46%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Filters.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.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::{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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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/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); ^~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 47%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.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/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:12: /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); ^~~~~~~~~~~~~~ [ 47%] Linking CXX executable smaTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 47%] Built target smaTest1 make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target Fingerprints make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 48%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 48%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread 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 /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target ChemTransforms [ 48%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/PatternFingerprints.cpp 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 /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h:35, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ /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 /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTWriter.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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:12: /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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.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 = {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>:: ^~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolWriters.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTWriter.cpp:16: /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTWriter.cpp: In destructor 'virtual RDKit::TDTWriter::~TDTWriter()': /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:104:11: warning: throw will always call terminate() [-Wterminate] throw inv; \ ^~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTWriter.cpp:64:5: note: in expansion of macro 'CHECK_INVARIANT' CHECK_INVARIANT(dp_ostream, ^~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:104:11: note: in C++11 destructors default to noexcept throw inv; \ ^~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TDTWriter.cpp:64:5: note: in expansion of macro 'CHECK_INVARIANT' CHECK_INVARIANT(dp_ostream, ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:29, 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h:16, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:12: /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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.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)...); ^~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:995:3: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ [ 49%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp In file included from /usr/include/c++/8/set:60, from /<>/rdkit-201709.3+dfsg/Code/Query/SetQuery.h:12, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:28, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.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 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:25, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.cpp:12: /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, In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:35, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Filters.h:35, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MACCS.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileParser.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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:17: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileParser.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>:: ^~~~~~~~~~~~~~~~~~~ /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:17: /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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~ [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/TplFileWriter.cpp make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 49%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -I/<>/rdkit-201709.3+dfsg/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/test1.cpp [ 49%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp [ 50%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2017.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target Fingerprints make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs2 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -I/<>/rdkit-201709.3+dfsg/External/boost-numeric-bindings -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/test2.cpp [ 50%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:24: /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h:16:21: warning: 'RDKit::ctdALL_FLAGS' defined but not used [-Wunused-variable] static unsigned int ctdALL_FLAGS = 0xFFFFFFFF; ^~~~~~~~~~~~ [ 50%] Linking CXX executable testSubgraphs1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target testSubgraphs1 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FragCatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:19: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:19: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:19: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:19: /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); ^~~~~~~~~~~~~~ [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp [ 50%] Linking CXX executable testSubgraphs2 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target testSubgraphs2 make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target testPartialCharges make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/test1.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h:14, from /<>/rdkit-201709.3+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 /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:34, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 50%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 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.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp: In function 'std::__cxx11::string RDKit::GetPDBBondLines(const RDKit::Atom*, bool, bool, bool, unsigned int&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp:163:20: warning: this statement may fall through [-Wimplicit-fallthrough=] v.push_back(dst); ~~~~~~~~~~~^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp:164:7: note: here case Bond::TRIPLE: ^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp:165:20: warning: this statement may fall through [-Wimplicit-fallthrough=] v.push_back(dst); ~~~~~~~~~~~^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp:166:7: note: here case Bond::DOUBLE: ^~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target FilterCatalog make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target rdPartialCharges make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 51%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 52%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 52%] Linking CXX executable testPartialCharges cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Built target testPartialCharges make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/PDBSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/functional/hash/extensions.hpp:22, from /usr/include/boost/functional/hash/hash.hpp:560, 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 /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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, [ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] Built target rdPartialCharges make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolChemicalFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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/functional/hash/extensions.hpp:22, from /usr/include/boost/functional/hash/hash.hpp:560, 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 /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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, [ 53%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.cpp:10: /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h:16:21: warning: 'RDKit::ctdALL_FLAGS' defined but not used [-Wunused-variable] static unsigned int ctdALL_FLAGS = 0xFFFFFFFF; ^~~~~~~~~~~~ [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceParsers.cpp [ 53%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h:13, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 53%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatParams.cpp [ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] Built target rdForceFieldHelpers make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdShapeHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 53%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.cpp [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2017.09.3 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/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Built target FileParsers make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/test1.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h: In function 'boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:31: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:43: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:55: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:31: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:43: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:55: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:31: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:43: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:55: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:31: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:43: 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) {} ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:55:55: 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/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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/functional/hash/extensions.hpp:22, from /usr/include/boost/functional/hash/hash.hpp:560, 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 /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h:17, from /<>/rdkit-201709.3+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, [ 54%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Built target rdShapeHelpers make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target rdReducedGraphs make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp [ 54%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2017.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2017.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Built target FragCatalog make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryTest make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/trajectoryTest.cpp [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 55%] Linking CXX executable testReducedGraphs cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 55%] Built target testReducedGraphs make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target SubstructLibrary make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 55%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/trajectoryTest.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 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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp: In function 'std::vector RDKit::{anonymous}::internalGetMatches(const RDKit::ROMol&, RDKit::MolHolderBase&, const RDKit::FPHolderBase*, unsigned int, unsigned int, bool, bool, bool, int, int)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp:150:14: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (endIdx < numThreads) numThreads = endIdx; ~~~~~~~^~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp: In function 'int RDKit::{anonymous}::internalMatchCounter(const RDKit::ROMol&, RDKit::MolHolderBase&, const RDKit::FPHolderBase*, unsigned int, unsigned int, bool, bool, bool, int)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp:203:14: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (endIdx < numThreads) numThreads = endIdx; ~~~~~~~^~~~~~~~~~~~ [ 56%] Linking CXX executable trajectoryTest cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 [ 57%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /<>/rdkit-201709.3+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++ -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitTrajectory.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Built target trajectoryTest make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= [ 57%] Built target rdReducedGraphs make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target testSLNParse make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/test.cpp [ 57%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 57%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Built target rdMolChemicalFeatures make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= Scanning dependencies of target rdchem make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/rdchem.cpp [ 57%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2017.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2017.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Built target SubstructLibrary make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Scanning dependencies of target rdtrajectory make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Trajectory.cpp [ 57%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization -lboost_regex ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Built target rdSLNParse [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/rdTrajectory.cpp make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolfiles make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/rdmolfiles.cpp [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/Table.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Table.cpp [ 58%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target rdtrajectory make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceField make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/testUFFForceField.cpp [ 59%] Linking CXX executable testSLNParse cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_regex ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] Built target testSLNParse make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DistGeom /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeometry make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistGeomUtils.cpp [ 59%] Linking CXX executable testUFFForceField cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] Built target testUFFForceField [ 59%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/TriangleSmooth.cpp [ 60%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Atom.cpp [ 60%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistViolationContrib.cpp [ 60%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 61%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/ChiralViolationContrib.cpp [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SDMolSupplier.cpp [ 62%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2017.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../lib/libRDKitForceField.so.1.2017.09.3 ../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target DistGeometry make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ForceField/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceField make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/Wrap/ForceField.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:23: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/TDTMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SmilesMolSupplier.cpp [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Bond.cpp [ 62%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SmilesWriter.cpp make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DistGeom /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeom make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/testDistGeom.cpp [ 64%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target rdForceField make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/DistGeom/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeom make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DDistGeom_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/DistGeom/Wrap/DistGeom.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept [ 64%] Linking CXX executable testDistGeom cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../lib/libRDKitForceField.so.1.2017.09.3 ../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target testDistGeom make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMolOpsTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/DistGeom/Wrap/DistGeom.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 = std::pair; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} 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/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/DistGeom/Wrap/DistGeom.cpp:12: /usr/include/c++/8/bits/stl_map.h: In function 'PyObject* RDKit::embedBoundsMatrix(boost::python::api::object, int, bool, int, boost::python::list, int)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SDWriter.cpp [ 64%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target DistGeom make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/test1.cpp [ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Mol.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp: In function 'void testGithub1281()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp:6911:16: warning: unused variable 'm' [-Wunused-variable] RWMol *m = SmilesToMol(smiles); ^ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/SDWriter.cpp:21: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.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>:: ^~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/TDTWriter.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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())); } ^ /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())); } ^ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/TDTWriter.cpp:21: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept [ 64%] Linking CXX executable graphmolTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../lib/libRDKitForceField.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPicklerGlobalSetting make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp /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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/PDBWriter.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp:10: /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); ^~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp: In function 'int main(int, char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp:256:14: warning: unused parameter 'argc' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp:256:26: warning: unused parameter 'argv' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~~~^~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp:10: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPicklerGlobalSettings.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>:: ^~~~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 65%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/PDBWriter.cpp:20: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Conformer.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/molopstest.cpp:10: /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); ^~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~ [ 65%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestChirality make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/testChirality.cpp /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ [ 65%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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/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.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target rdmolfiles make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPickler make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPickler.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Conformer.cpp:20: /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void RDKit::SetAtomPos(RDKit::Conformer*, unsigned int, boost::python::api::object)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: 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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/Conformer.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); ^~~~~~~~~~~~~~ [ 66%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/RingInfo.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPickler.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPickler.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/testPickler.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)...); ^~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/EditableMol.cpp [ 67%] Linking CXX executable graphmoltestPickler cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 67%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= Scanning dependencies of target molBundleTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/testMolBundle.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/EditableMol.cpp:22: /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/EditableMol.cpp: In destructor 'RDKit::{anonymous}::EditableMol::~EditableMol()': /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:112:11: warning: throw will always call terminate() [-Wterminate] throw inv; \ ^~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:112:11: note: in definition of macro 'PRECONDITION' throw inv; \ ^~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:112:11: note: in C++11 destructors default to noexcept throw inv; \ ^~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:112:11: note: in definition of macro 'PRECONDITION' throw inv; \ ^~~ [ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/MonomerInfo.cpp [ 67%] Linking CXX executable graphmoltestChirality cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 67%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= Scanning dependencies of target hanoiTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/hanoitest.cpp [ 68%] Linking CXX executable graphmolMolOpsTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 68%] Built target graphmolMolOpsTest make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= Scanning dependencies of target resMolSupplierTest make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/resMolSupplierTest.cpp [ 69%] Linking CXX executable molBundleTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 69%] Built target molBundleTest make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target testDepictor make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 69%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/testDepictor.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/new_canon.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/hanoitest.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 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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:60, from /<>/rdkit-201709.3+dfsg/Code/Query/SetQuery.h:12, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:28, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:12: /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>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 69%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 69%] Linking CXX executable resMolSupplierTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread [ 70%] Linking CXX executable hanoiTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 70%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target rdDepictor make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' /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>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp In file included from /usr/include/c++/8/map:61, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:25, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:12: /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, make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/set:60, from /<>/rdkit-201709.3+dfsg/Code/Query/SetQuery.h:12, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:28, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:12: /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); ^~~~~~~~~~~~ [ 70%] Built target hanoiTest [ 70%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/MolBundle.cpp In file included from /usr/include/c++/8/map:61, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:25, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:12: /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, /usr/include/c++/8/bits/stl_map.h: In function 'void testIssue3135833()': /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, [ 71%] Linking CXX executable testDepictor cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/smiTest1.dir/test.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/test.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/test.cpp: In function 'void testFail()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/test.cpp:165:14: warning: catching polymorphic type 'class RDKit::MolSanitizeException' by value [-Wcatch-value=] } catch (MolSanitizeException) { ^~~~~~~~~~~~~~~~~~~~ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:17: /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:288:15: warning: '*((void*)(&)+16).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/cxsmiles_test.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/test.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>:: ^~~~~~~~~~~~~~~~~~~ [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target rdDepictor make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= Scanning dependencies of target testSequence make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testSequence.cpp [ 73%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target rdchem make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= Scanning dependencies of target fileParsersTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/test1.cpp [ 73%] Linking CXX executable testSequence cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= Scanning dependencies of target testMolSupplier make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 73%] Linking CXX executable cxsmilesTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= Scanning dependencies of target testMolWriter make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testMolSupplier.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::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 In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/test1.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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/test1.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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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/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/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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/test1.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 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)...); ^~~~~~~~~~~~~~~~~ /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:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testMolSupplier.cpp:11: /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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ [ 74%] Linking CXX executable testMolSupplier cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= Scanning dependencies of target testTplParser make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testTpls.cpp [ 74%] Linking CXX executable testMolWriter cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= Scanning dependencies of target testMol2ToMol make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 75%] Linking CXX executable smiTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Built target smiTest1 make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= Scanning dependencies of target testSubstructMatch make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/test1.cpp [ 75%] Linking CXX executable testTplParser cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Built target testTplParser make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= Scanning dependencies of target Descriptors make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Crippen.cpp [ 75%] Linking CXX executable testMol2ToMol cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Built target testMol2ToMol make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testChemTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 75%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/testChemTransforms.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Crippen.cpp: In constructor 'RDKit::Descriptors::CrippenParamCollection::CrippenParamCollection(const string&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Crippen.cpp:172:25: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] } catch (boost::bad_lexical_cast) { ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/test1.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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolDescriptors.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)...); ^~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 76%] Linking CXX executable testSubstructMatch cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target testSubstructMatch make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= Scanning dependencies of target filterCatalogTest make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolSurf.cpp /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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolSurf.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)...); ^~~~~~~~~~~~~~~~~ [ 76%] Linking CXX executable fileParsersTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target fileParsersTest1 make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfiltercatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 76%] Linking CXX executable testChemTransforms cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/filtercatalogtest.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 [ 76%] Built target testChemTransforms [ 77%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp /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)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void testFilterCatalogEntry()': /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)...); ^~~~~~~~~~~~~~~~~ [ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Lipinski.cpp [ 77%] Linking CXX executable filterCatalogTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] Built target filterCatalogTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target testFragCatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/test1.cpp make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfragcatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp [ 77%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 78%] Linking CXX executable testFragCatalog cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 78%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target testFingerprints make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 78%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/test1.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:26, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MQN.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Property.cpp [ 78%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ /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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Property.h:35, from /<>/rdkit-201709.3+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>::_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 /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)...); ^~~~~~~~~~~~~~~~~ /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::Descriptors::Properties::annotateProperties(RDKit::ROMol&) 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)...); ^~~~~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp [ 79%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp: In function 'void RDKit::Descriptors::{anonymous}::get2DautocorrelationDesc(double*, int, const RDKit::ROMol&, std::vector&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp:60:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for (unsigned int i = 0; i < numAtoms; i++) { ~~^~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp:69:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for (unsigned int i = 0; i < numAtoms; i++) { ~~^~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp:77:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for (unsigned int i = 0; i < numAtoms; i++) { ~~^~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp:92:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for (unsigned int i = 0; i < numAtoms; ++i) { ~~^~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp:93:38: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for (unsigned int j = i + 1; j < numAtoms; ++j) { ~~^~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp [ 80%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lboost_serialization -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Built target rdfiltercatalog make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testMolTransforms make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/test1.cpp [ 80%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/USRDescriptor.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/test1.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/test1.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); ^~~~~~~~~~~~~~ [ 80%] Linking CXX executable testFingerprints cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Built target testFingerprints make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testFeatures make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.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); ^~~~~~~~~~~~~~ [ 80%] Linking CXX executable testMolTransforms cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Built target testMolTransforms make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testShapeHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp [ 81%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2017.09.3 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.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread [ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target rdfragcatalog [ 81%] Built target Descriptors 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 make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolCatalog Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/<>/rdkit-201709.3+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]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o [ 82%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/test1.cpp cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.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); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void test6()': /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); ^~~~~~~~~~~~~~ [ 82%] Linking CXX executable testShapeHelpers cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2017.09.3 ../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 82%] Built target testShapeHelpers make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Scanning dependencies of target FMCS make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/FMCS.cpp [ 83%] Linking CXX executable testFeatures cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 83%] Built target testFeatures make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= Scanning dependencies of target MolHash make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/MolHash.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolHash.dir/MolHash.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/MolHash.cpp [ 84%] Linking CXX executable testMolCatalog cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] Built target testMolCatalog make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= Scanning dependencies of target MMPA make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DMMPA_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA.cpp [ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] Built target rdMolCatalog make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target StructChecker make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructChecker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/StructChecker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp [ 85%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/HashToString.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolHash.dir/HashToString.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/HashToString.cpp [ 86%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Seed.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp: In member function 'unsigned int RDKit::StructureCheck::StructChecker::checkMolStructure(RDKit::RWMol&) const': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:51:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:60:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:68:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:85:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:122:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp:130:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ [ 86%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2017.09.3 CMakeFiles/MolHash.dir/MolHash.cpp.o CMakeFiles/MolHash.dir/HashToString.cpp.o ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2017.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 86%] Built target MolHash make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= Scanning dependencies of target substructLibraryTest make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 86%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2017.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2017.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 86%] Built target MMPA make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target rdSubstructLibrary make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 87%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp: In function 'bool RDKit::StructureCheck::parseOptionsJSON(const string&, RDKit::StructureCheck::StructCheckerOptions&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp:33:19: warning: unused variable 'iss' [-Wunused-variable] std::istream &iss = ss; ^~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp: In function 'bool RDKit::StructureCheck::ReadAAPairs(const string&, std::vector >&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp:356:12: warning: unused variable 'k' [-Wunused-variable] unsigned k = fscanf(fp, "%d", &n); ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp: In function 'bool RDKit::StructureCheck::loadChargeDataTables(const string&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp:666:46: warning: unused parameter 'path' [-Wunused-parameter] bool loadChargeDataTables(const std::string &path) { ~~~~~~~~~~~~~~~~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp: In function 'int main(int, char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp:191:14: warning: unused parameter 'argc' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp:191:26: warning: unused parameter 'argv' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~~~^~~~~~ [ 87%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 87%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 87%] Linking CXX executable substructLibraryTest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target substructLibraryTest make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructureFlags.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructureFlags.cpp [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Utilites.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/Utilites.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Utilites.cpp [ 88%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 88%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 88%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Pattern.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/Pattern.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp [ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] Built target rdSubstructLibrary make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target ChemReactions make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp: In function 'void RDKit::StructureCheck::applyAtomSymbolList(RDKit::RWMol&, std::__cxx11::string, RDKit::Atom&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:96:15: warning: unused variable 'atsym' [-Wunused-variable] const char *atsym = symbol.c_str(); ^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp: In function 'bool RDKit::StructureCheck::TransformAugmentedAtoms(RDKit::RWMol&, const std::vector >&, bool)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:216:11: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp: In function 'bool RDKit::StructureCheck::RecMatch(const RDKit::ROMol&, unsigned int, const RDKit::StructureCheck::AugmentedAtom&, const std::vector&, bool)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:374:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp: In function 'bool RDKit::StructureCheck::CheckAtoms(const RDKit::ROMol&, const std::vector&, bool)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:546:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (verbose && //j >= 12 && j <= 21 && ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:555:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (verbose && //j >= 12 && j <= 21 && ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.cpp:588:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (verbose && nmatch == prevn) // UNMATCHED atom ^ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h:15, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 88%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2017.09.3 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/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h:15, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] Built target FMCS make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target testDescriptors make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/test.cpp [ 89%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Stereo.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/Stereo.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp /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); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 89%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp: In function 'int RDKit::StructureCheck::DubiousStereochemistry(RDKit::RWMol&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp:136:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses] (14 == element && // "Si" ~~~~~~~~~~~~~~~~~~~~~~~~~~ n_ligands > 2 && n_ligands <= 4) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ nmulti == 0)) ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp: In function 'int RDKit::StructureCheck::FixDubious3DMolecule(RDKit::RWMol&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp:222:56: warning: suggest parentheses around '&&' within '||' [-Wparentheses] RDKit::Bond::BEGINDASH == bond->getBondDir() && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ i == bond->getBeginAtomIdx()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp: In function 'void RDKit::StructureCheck::RemoveDubiousStereochemistry(RDKit::RWMol&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp:334:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses] (14 == element && // "Si" ~~~~~~~~~~~~~~~~~~~~~~~~~~ n_ligands > 2 && n_ligands <= 4) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ nmulti == 0)) { ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp: In function 'int RDKit::StructureCheck::Atom3Parity(RDKit::StructureCheck::stereo_bond_t*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.cpp:373:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (ligands[i].direction != RDKit::Bond::NONE) ^ cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target DistGeomHelpers [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/MDLParser.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/test.cpp: In function 'void testProperties()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/test.cpp:1909:14: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] } catch (KeyErrorException) { ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/test.cpp: In function 'void testStereoCounting()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/test.cpp:1957:12: warning: catching polymorphic type 'class ValueErrorException' by value [-Wcatch-value=] } catch (ValueErrorException) { ^~~~~~~~~~~~~~~~~~~ [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 89%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/AtomSymbolMatch.cpp [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionWriter.cpp [ 90%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionWriter.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 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)...); ^~~~~~~~~~~~~~~~~ [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionDepict.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/../MolOps.h:14, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 90%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/ReCharge.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp: In member function 'bool RDKit::StructureCheck::ChargeFix::setpKaValues()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp:166:24: warning: variable 'AAp' set but not used [-Wunused-but-set-variable] const AugmentedAtom *AAp; ^~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp: In member function 'int RDKit::StructureCheck::ChargeFix::markMostAcidicAtoms(double&, double&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp:416:17: warning: unused variable 'atom' [-Wunused-variable] const Atom &atom = *Mol.getAtomWithIdx(i); ^~~~ [ 90%] Linking CXX executable testDescriptors cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 90%] Built target testDescriptors [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 90%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/StructChecker.dir/Tautomer.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp [ 90%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp: In member function 'bool RDKit::StructureCheck::StructCheckTautomer::applyTautomer(unsigned int)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:20:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:28:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:44:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (Options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if (-1 == ti || -1 == tj) continue; ~~~^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:61:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if (-1 == ti || -1 == tj) continue; ~~~^~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp:36:18: warning: unused variable 'ntb' [-Wunused-variable] const unsigned ntb = toTautomer.getNumBonds(); ^~~ [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.cpp [ 91%] Linking CXX shared library ../../../lib/libRDKitStructChecker.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitStructChecker.so.1 -o ../../../lib/libRDKitStructChecker.so.1.2017.09.3 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/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitStructChecker.so.1.2017.09.3 ../../../lib/libRDKitStructChecker.so.1 ../../../lib/libRDKitStructChecker.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target StructChecker make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= Scanning dependencies of target testAUTOCORR2D make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp: In function 'int main(int, char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp:87:14: warning: unused parameter 'argc' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp:87:26: warning: unused parameter 'argv' [-Wunused-parameter] int main(int argc, char *argv[]) { ~~~~~~^~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:35, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.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: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)...); ^~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable testAUTOCORR2D cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target testAUTOCORR2D make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDescriptors make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 91%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:20, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h:35, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:35, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp:32: /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp: In member function 'virtual void RDKit::EvenSamplePairsStrategy::initializeStrategy(const RDKit::ChemicalReaction&, const BBS&)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp:69:34: warning: comparison of unsigned expression >= 0 is always true [-Wtype-limits] PRECONDITION(m_numPermutations >= 0, ~~~~~~~~~~~~~~~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h:108:9: note: in definition of macro 'PRECONDITION' if (!(expr)) { \ ^~~~ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/format/parsing.hpp:21, from /usr/include/boost/format.hpp:50, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp:33: /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp: In member function 'bool RDKit::EvenSamplePairsStrategy::try_add(size_t)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp:149:31: warning: comparison of unsigned expression >= 0 is always true [-Wtype-limits] assert(var_used[i][j] >= 0); make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testMMFFForceFieldHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceFieldHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 92%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2017.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 92%] Built target ChemReactions make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 92%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:84:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:84:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable testCrystalForceField cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 92%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeomHelpers make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 92%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 93%] Linking CXX executable testMMFFForceFieldHelpers cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target rdDistGeom make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 93%] Linking CXX executable testUFFForceFieldHelpers cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.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 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>:: ^~~~~~~~~~~~~~~~~~~ [ 93%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target testMolAlign make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/testMolAlign.cpp /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 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/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:16: /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:84:15: 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/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h:13, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h:36, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h:18, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:16: /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h:84:15: 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/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+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, [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target rdMolDescriptors make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolAlign make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In function 'void testTemp()': /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); ^~~~~~~~~~~~~~~~~ [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Vector.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/Matrix.h:14, from /<>/rdkit-201709.3+dfsg/Code/Numerics/SquareMatrix.h:13, from /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform3D.h:15, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h:13, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target rdDistGeom make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp [ 93%] Linking CXX executable testDistGeomHelpers cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target testDistGeomHelpers make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target testFMCS make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/testFMCS_Unit.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp: In function 'void RDKit::{anonymous}::get2DCoordsForReaction(RDKit::ChemicalReaction&, const RDKit::MolDrawOptions&, RDGeom::Point2D&, RDGeom::Point2D&, std::vector&, double, const std::vector*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:405:74: warning: unused parameter 'opts' [-Wunused-parameter] void get2DCoordsForReaction(ChemicalReaction &rxn, const MolDrawOptions &opts, ~~~~~~~~~~~~~~~~~~~~~~^~~~ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:457:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(prbCrippenContribs) == prbNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:472:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(refCrippenContribs) == refNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:540:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(prbCrippenContribs) == prbNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:555:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(refCrippenContribs) == refNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 93%] Linking CXX executable testMolAlign cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target testMolAlign make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target rdFMCS make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+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>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:18, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:18, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:18, from /<>/rdkit-201709.3+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 = {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>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {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 In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:23: /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'RDNumeric::DoubleVector* RDKit::_translateWeights(boost::python::api::object)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h:67:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /usr/include/c++/8/bits/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)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::MolDraw2D::extractAtomCoords(const RDKit::ROMol&, int, 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)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void test18()': /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 RDKit::Atom::setAtomMapNum(int, 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)...); ^~~~~~~~~~~~~~~~~ [ 93%] Linking CXX executable testFMCS cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target testFMCS make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= In file included from /usr/include/c++/8/vector:64, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:18, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /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); ^~~~~~~~~~~~~~~~~ Scanning dependencies of target FMCStest make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::__cxx11::string testChEMBL_Txt(const char*, double, const char*)': /<>/rdkit-201709.3+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, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1174:21: 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(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1186:21: 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(), ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1281:23: 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(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1330:21: 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(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1411:23: 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(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp [ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../../lib/libRDKitAlignment.so.1.2017.09.3 ../../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target rdMolAlign make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target testMolHash make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/testMolHash.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMolHash.dir/testMolHash.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/testMolHash.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/../../RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:47: /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>:: ^~~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolHash make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp: In member function 'virtual void RDKit::MolDraw2DSVG::drawWavyLine(const RDGeom::Point2D&, const RDGeom::Point2D&, const DrawColour&, const DrawColour&, unsigned int, double)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp:72:75: warning: unused parameter 'col2' [-Wunused-parameter] const DrawColour &col1, const DrawColour &col2, ~~~~~~~~~~~~~~~~~~^~~~ /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)...); ^~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable FMCStest cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Built target FMCStest make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target testMMPA make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 95%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp [ 95%] Linking CXX executable testMolHash cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolHash.dir/testMolHash.cpp.o -o testMolHash ../../../lib/libRDKitMolHash.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target rdMMPA make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:14, from /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:14, from /<>/rdkit-201709.3+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); ^~~~~~~~~~~~~~~~~ [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2017.09.3 ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Built target rdMolHash make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target testStructChecker make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp [ 95%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp [ 95%] Linking CXX executable testMMPA cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target rdStructChecker make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdStructChecker_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Wrap/structchecker.cpp /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void doLoadOptionsFromFiles(RDKit::StructureCheck::StructCheckerOptions&, const string&, bool)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:98:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:101:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:106:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:111:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:122:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:127:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (options.Verbose) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testLoadOptionsFromFiles()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:139:8: warning: unused variable 'ok' [-Wunused-variable] bool ok; ^~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void test1()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:168:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void test2()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:195:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testStereo()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:324:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testOptionsDefault()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:400:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testCheckAtomWithDefaultGoodAtoms()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:424:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testCheckAtom()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:448:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testCheckMatch()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:539:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (!CheckAtoms(*mol, options.GoodAtoms, options.Verbose)) ^ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testSpecificExamples()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:603:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testSpecificOrder()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:676:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testTransformTau()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:705:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testTransformAtoms()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:749:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'void testAugmentedAtomTranslationsToAtomListQuery()': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:787:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < sizeof(smols) / sizeof(smols[0]); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp: In function 'int main(int, const char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:844:14: warning: unused parameter 'argc' [-Wunused-parameter] int main(int argc, const char* argv[]) { ~~~~^~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/testStructChecker.cpp:844:32: warning: unused parameter 'argv' [-Wunused-parameter] int main(int argc, const char* argv[]) { ~~~~~~~~~~~~^~~~~~ [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Built target rdMMPA make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target RGroupDecomposition make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp [ 96%] Linking CXX executable testStructChecker cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -o testStructChecker ../../../lib/libRDKitStructChecker.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target testStructChecker make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testMMFFForceField make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/testMMFFForceField.cpp [ 96%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2017.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lboost_serialization cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2017.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target MolDraw2D make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= Scanning dependencies of target testReaction make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp [ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdStructChecker.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdStructChecker.so CMakeFiles/rdStructChecker.dir/structchecker.cpp.o ../../../../lib/libRDKitStructChecker.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target rdStructChecker make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= Scanning dependencies of target testEnumeration make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/Query/Query.h:17, from /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h:19, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h:24, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:22, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:13, from /<>/rdkit-201709.3+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)...); ^~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp: In function 'int main(int, char**)': /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp:372:8: warning: variable 'doLong' set but not used [-Wunused-but-set-variable] bool doLong = false; ^~~~~~ [ 96%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2017.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o ../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2017.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target RGroupDecomposition make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target testReactionFingerprints make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/testReaction.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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp:33: /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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/testReaction.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)...); ^~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable testMMFFForceField cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2017.09.3 ../../../lib/libRDKitDistGeometry.so.1.2017.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2017.09.3 ../../../lib/libRDKitForceField.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitMolAlign.so.1.2017.09.3 ../../../lib/libRDKitOptimizer.so.1.2017.09.3 ../../../lib/libRDKitAlignment.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] 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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemReactions make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Linking CXX executable testEnumeration cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 [ 97%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target testEnumeration make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/test1.cpp [ 97%] Linking CXX executable testReactionFingerprints cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target testReactionFingerprints make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/rxn_test1.cpp In file included from /usr/include/c++/8/vector:69, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:20, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/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>:: ^~~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable moldraw2DRxnTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+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 make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDraw2D make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.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)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/test1.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 = 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 /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h:18, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h:21, from /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h:14, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/test1.cpp:11: /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, [ 98%] Linking CXX executable moldraw2DTest1 cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 98%] Built target moldraw2DTest1 make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.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 = {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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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); ^~~~~~~~~~~~~~~~~ /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); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.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, 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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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:13, 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 /<>/rdkit-201709.3+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: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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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/python/suite/indexing/detail/indexing_suite_detail.hpp:15, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /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 /<>/rdkit-201709.3+dfsg/Code/RDBoost/Wrap.h:55, from /<>/rdkit-201709.3+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 [ 99%] Linking CXX executable testRGroupDecomp cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2017.09.3 ../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target testRGroupDecomp make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target rdRGroupDecomposition make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 99%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp In file included from /usr/include/c++/8/map:60, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.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 = 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>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': /<>/rdkit-201709.3+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]); ^ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h:4, from /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: /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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:46: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept [ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2017.09.3 ../../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system -lboost_serialization make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target rdMolDraw2D make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/rdkit-201709.3+dfsg /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolops make[4]: Leaving directory '/<>/rdkit-201709.3+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 '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/rdmolops.cpp [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2017.09.3 ../../../../lib/libRDKitFMCS.so.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target rdRGroupDecomposition [ 99%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/usr/include/python2.7 -I/<>/rdkit-201709.3+dfsg/Code -g -O2 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/MolOps.cpp In file included from /<>/rdkit-201709.3+dfsg/Code/GraphMol/Wrap/MolOps.cpp:30: /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In destructor 'virtual boost_adaptbx::python::ostream::~ostream()': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: warning: throw will always call terminate() [-Wterminate] " returning."); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:470:24: note: in C++11 destructors default to noexcept [ 99%] Linking CXX executable testReaction cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lboost_thread -lboost_system -lpthread make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target testReaction [100%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lboost_serialization -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [100%] Built target rdChemReactions /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:184:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:154:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /<>/rdkit-201709.3+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)': /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h:335:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /<>/rdkit-201709.3+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 -fdebug-prefix-map=/<>/rdkit-201709.3+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 -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.1.2017.09.3 ../../../lib/libRDKitRDBoost.so.1.2017.09.3 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lboost_chrono -lboost_date_time -lboost_atomic -lpthread -lboost_serialization ../../../lib/libRDKitChemReactions.so.1.2017.09.3 ../../../lib/libRDKitFingerprints.so.1.2017.09.3 ../../../lib/libRDKitChemTransforms.so.1.2017.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2017.09.3 ../../../lib/libRDKitCatalogs.so.1.2017.09.3 ../../../lib/libRDKitDescriptors.so.1.2017.09.3 ../../../lib/libRDKitPartialCharges.so.1.2017.09.3 ../../../lib/libRDKitDepictor.so.1.2017.09.3 ../../../lib/libRDKitFileParsers.so.1.2017.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2017.09.3 ../../../lib/libRDKitSubgraphs.so.1.2017.09.3 ../../../lib/libRDKitSmilesParse.so.1.2017.09.3 ../../../lib/libRDKitMolTransforms.so.1.2017.09.3 ../../../lib/libRDKitGraphMol.so.1.2017.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2017.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2017.09.3 ../../../lib/libRDKitDataStructs.so.1.2017.09.3 ../../../lib/libRDKitRDGeneral.so.1.2017.09.3 -lpthread -lboost_thread -lboost_system -lboost_serialization make[4]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' [100%] Built target rdmolops make[3]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' (cd /<>/rdkit-201709.3+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 /<>/rdkit-201709.3+dfsg/Code/GraphMol Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Test Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/libs Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/QTDemo Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Catalogs Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/DataStructs Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Query Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ML Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ML/Cluster Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ML/Cluster/Murtagh Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ML/Data Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/DataManip Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/SimDivPickers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/RDGeneral Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/RDGeneral/hash Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/RDGeneral/hash/detail Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/RDBoost Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/DistGeom Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ForceField Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Numerics Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Numerics/EigenSolvers Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Geometry Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/Features Searching for files in directory /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/atomic_data.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/atomic_data.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/AtomIterators.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/AtomIterators.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Bond.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Bond.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/BondIterators.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/BondIterators.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Canon.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Canon.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Chirality.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Chirality.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Conformer.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Crippen.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MORSE.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MQN.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/MQN.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/PBF.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/PBF.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/PMI.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/PMI.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Property.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Property.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/RDF.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/RDF.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/WHIM.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/details.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/details.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Composition2N.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/FMCS.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/FMCS.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Graph.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Graph.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/MatchTable.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/RingMatchTableSet.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/RingMatchTableSet.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Seed.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Seed.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SeedSet.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Target.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/Target.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/GraphMol.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolBundle.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolBundle.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/DrawingToCairo.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/DrawingToCairo.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/DrawingToSVG.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/DrawingToSVG.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/MolDrawing.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDrawing/MolDrawing.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/MolHash.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolHash/MolHash.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolPickler.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolPickler.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/MonomerInfo.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MonomerInfo.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/new_canon.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/new_canon.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/PeriodicTable.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/PeriodicTable.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryAtom.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryAtom.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryBond.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryBond.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitBase.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitQueries.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/RDKitQueries.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Resonance.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Resonance.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/RingInfo.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/RingInfo.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Rings.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Rings.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ROMol.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/RWMol.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SanitException.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SanitException.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/primes.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/primes.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Utilites.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Catalogs/Catalog.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogEntry.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogEntry.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogParams.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Catalogs/CatalogParams.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/base64.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/base64.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVect.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVect.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVects.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVects.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVectUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitVectUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/DatastructsException.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/DatastructsException.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteDistMat.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteDistMat.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteValueVect.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/DiscreteValueVect.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/ExplicitBitVect.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/FPBReader.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/FPBReader.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/MultiFPBReader.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/MultiFPBReader.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/SparseBitVect.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/SparseBitVect.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataStructs/SparseIntVect.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataStructs/SparseIntVect.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/AndQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/AndQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/EqualityQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/EqualityQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/GreaterEqualQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/GreaterEqualQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/GreaterQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/GreaterQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/LessEqualQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/LessEqualQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/LessQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/LessQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/OrQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/OrQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/Query.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/Query.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/QueryObjects.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/RangeQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/RangeQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/SetQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/SetQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Query/XOrQuery.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Query/XOrQuery.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/DistPicker.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/DistPicker.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/MaxMinPicker.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BadFileException.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BoostEndInclude.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BoostEndInclude.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BoostStartInclude.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/BoostStartInclude.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Dict.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Exceptions.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Exceptions.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/FileParseException.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/FileParseException.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/hanoiSort.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/hanoiSort.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Invariant.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/LocaleSwitcher.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Ranking.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/Ranking.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDAny.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDAny.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDLog.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDProps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDProps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDThreads.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDThreads.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/RDValue.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/StreamOps.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/StreamOps.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/types.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/utils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDGeneral/versions.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDGeneral/versions.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/boost_numpy.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/boost_numpy.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/import_array.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/import_array.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/iterator_next.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/iterator_next.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/pyint_api.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/pyint_api.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/PySequenceHolder.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/python.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/RDBoost/python_streambuf.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/BoundsMatrix.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/BoundsMatrix.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/ChiralSet.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/ChiralSet.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/ChiralViolationContrib.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistGeomUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistGeomUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistViolationContrib.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/DistViolationContrib.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/FourthDimContrib.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/FourthDimContrib.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/DistGeom/TriangleSmooth.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/DistGeom/TriangleSmooth.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/Contrib.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/Contrib.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleBend.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleBend.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Contribs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Contribs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Nonbonded.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/OopBend.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/OopBend.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/StretchBend.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/StretchBend.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleBend.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleBend.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/BondStretch.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/BondStretch.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Contribs.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Contribs.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Inversion.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Inversion.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Nonbonded.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Nonbonded.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Params.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Params.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/PositionConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionAngle.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/AlignPoints.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/Matrix.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/Matrix.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/SquareMatrix.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/SquareMatrix.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/SymmMatrix.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/SymmMatrix.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Numerics/Vector.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Numerics/Vector.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/Grid3D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/Grid3D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/GridUtils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/GridUtils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/point.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform2D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry//<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Contribs.h:14: warning: the name `Contribs.h' supplied as the second argument in the \file statement matches the following input files: /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Contribs.h /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Contribs.h Please use a more specific name by including a (larger) part of the path! /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Contribs.h:12: warning: the name `Contribs.h' supplied as the second argument in the \file statement matches the following input files: /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Contribs.h /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Contribs.h Please use a more specific name by including a (larger) part of the path! Transform2D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform3D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/Transform3D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/UniformGrid3D.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/UniformGrid3D.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Geometry/Utils.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Geometry/Utils.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/Features/Feature.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/Features/Feature.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /<>/rdkit-201709.3+dfsg/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /<>/rdkit-201709.3+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 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 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 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 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 DrawingToCairo.h... Generating code for file DrawingToSVG.h... Generating code for file DuplicatedSeedCache.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 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 Fingerprints.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 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 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 MolDrawing.h... Generating code for file MolFileStereochem.h... Generating code for file MolFragmenter.h... Generating code for file MolHash.h... Generating code for file MolOps.h... Generating code for file MolPickler.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 MORSE.h... Generating code for file MQN.h... Generating code for file MultiFPBReader.h... Generating code for file new_canon.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.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 RDDepictor.h... Generating code for file RDF.h... Generating code for file RDKitBase.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... /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitOps.h:173: warning: found at different nesting level (7) than expected (4) /<>/rdkit-201709.3+dfsg/Code/DataStructs/BitOps.h:174: warning: end of comment block while expecting command 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 StreamOps.h... Generating code for file StretchBend.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.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 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 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 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 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 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 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 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 DrawingToCairo.h... Generating docs for file DrawingToSVG.h... Generating docs for file DuplicatedSeedCache.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 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 Fingerprints.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 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 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 MolCatalog.h... Generating docs for file MolCatalogEntry.h... Generating docs for file MolCatalogParams.h./<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:367: warning: Found unknown command `\overloadquery' /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:376: warning: Found unknown command `\overloadquery' .. 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 MolDrawing.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolFragmenter.h... Generating docs for file MolHash.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.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 MORSE.h... Generating docs for file MQN.h... Generating docs for file MultiFPBReader.h... Generating docs for file new_canon.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.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 RDDepictor.h... Generating docs for file RDF.h... Generating docs for file RDKitBase.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 doc/<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h:132: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h:138: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/ForceField.h:138: 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) s 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 StreamOps.h... Generating docs for file StretchBend.h... Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.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 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 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 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 compound boost_adaptbx::python::streambuf::ostream... Generating docs for compound boost_adaptbx::python::streambuf_capsule... Generating docs for namespace ChemicalFeatures Generating docs for compound ChemicalFeatures::ChemicalFeature... Generating docs for compound ChemicalFeatures::FreeChemicalFeature... Generating docs for namespace 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::TorsionA/<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleBend.h:30: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleBend.h:39: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.h:26: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.h:26: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/AngleConstraint.h:35: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h:27: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h:27: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h:27: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/BondStretch.h:35: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Nonbonded.h:58: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:160: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:176: warning: The following parameters of ForceFields::MMFF::MMFFAromCollection::getMMFFArom(const boost::uint8_t *aromatic_types=NULL) are not documented: parameter 'aromatic_types' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:1085: warning: The following parameters of ForceFields::MMFF::MMFFOopCollection::getMMFFOop(const bool isMMFFs=false, const std::string &mmffOop="") are not documented: parameter 'isMMFFs' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Params.h:1214: warning: The following parameters of ForceFields::MMFF::MMFFTorCollection::getMMFFTor(const bool isMMFFs, const std::string &mmffTor="") are not documented: parameter 'isMMFFs' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/PositionConstraint.h:27: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/StretchBend.h:31: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/StretchBend.h:40: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionAngle.h:33: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/TorsionAngle.h:44: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/MMFF/Nonbonded.h:34: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.h:26: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.h:26: 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) /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/AngleConstraint.h:35: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/Inversion.h:38: 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' /<>/rdkit-201709.3+dfsg/Code/ForceField/UFF/PositionConstraint.h:27: 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) ngleContribM6... 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 compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransfo/<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h:163: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/Depictor/RDDepictor.h:182: warning: The following parameters of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=0, bool acceptFailure=false) are not documented: parameter 'referencePattern' /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:367: warning: Found unknown command `\overloadquery' /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:376: warning: Found unknown command `\overloadquery' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h:93: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h:98: warning: The following parameters of RDKit::HELMToMol(const char *helm, bool sanitize=true) are not documented: parameter 'helm' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:104: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:367: warning: Found unknown command `\overloadquery' /<>/rdkit-201709.3+dfsg/Code/GraphMol/QueryOps.h:376: warning: Found unknown command `\overloadquery' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:228: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/FileParsers.h:239: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:235: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:235: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:235: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:235: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:25: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:52: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:93: warning: The following parameters of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) are not documented: parameter 'product' /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:110: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:61: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:74: 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' rms 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::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::atomicData... 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... 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::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::EnumerationStrat/<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:414: 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 99 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:414: warning: The following parameters of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:99: 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 /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:105: warning: The following parameters of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 are not documented: parameter 'matchVect' /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:175: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:206: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:206: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:206: 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) /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:230: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Resonance.h:55: 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) egyBase... 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::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... 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::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.../<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:321: 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 99 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:321: warning: The following parameters of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:195: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:195: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:195: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:195: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /<>/rdkit-201709.3+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:195: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h:160: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h:210: warning: The following parameters of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< boost::uint32_t > &atomCodes, bool includeChirality=false) are not documented: parameter 'includeChirality' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Canon.h:112: 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) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Lipinski.h:44: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/Lipinski.h:51: warning: The following parameters of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) are not documented: parameter 'useStrictDefinition' /<>/rdkit-201709.3+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h:78: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:85: 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 99 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:85: warning: The following parameters of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:203: 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 99 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:203: warning: The following parameters of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:147: 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 99 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /<>/rdkit-201709.3+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:147: warning: The following parameters of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' 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::SubstructLibrary... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... 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 docs for namespace RDKit::detail Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::Drawing Generating docs for namespace RDKit::Drawing::detail 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/<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA.h:35: 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;!$(*=,#[!#6])]!@!=!#[*]") are not documented: parameter 'pattern' /<>/rdkit-201709.3+dfsg/Code/GraphMol/MMPA/MMPA.h:56: warning: The following parameters of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") are not documented: parameter 'pattern' /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.h:616: 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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolOps.h:241: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false) are not documented: parameter 'mergeUnmappedOnly' /<>/rdkit-201709.3+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' /<>/rdkit-201709.3+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:33: warning: The following parameters of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=0) are not documented: parameter 'atomTypes' /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:123: 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()) /<>/rdkit-201709.3+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:154: 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' /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h:79: warning: The following parameters of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const are not documented: parameter 'distMat' /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/MaxMinPicker.h:53: 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 /<>/rdkit-201709.3+dfsg/Code/SimDivPickers/MaxMinPicker.h:53: 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 ::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::MolOps Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MorganFingerprints Generating docs for namespace RDKit::PicklerOps 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::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 13052/65536 hits=109516 misses=14181 finished... (cd /<>/rdkit-201709.3+dfsg/rdkit; epydoc --config epydoc.config) [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FastSDMolSupplier.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | SaltRemover.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/QED.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Recap.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FragmentMatcher.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolSurf.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | PeriodicTable.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | ChemicalFeatures.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | TorsionFingerprints.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | BuildFragmentCatalog.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | EnumerateStereoisomers.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MCS.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Crippen.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Randomize.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ShowMols.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | Descriptors.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FilterCatalog.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolCatalog.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AllChem.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MACCSkeys.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Lipinski.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | ChemicalForceFields.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/inchi.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | PandasTools.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FunctionalGroups.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fragments.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Graphs.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FeatFinderCLI.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/PyMol.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | TemplateAlign.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | PropertyMol.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | GraphDescriptors.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | ReducedGraphs.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | Descriptors3D.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/BRICS.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/SATIS.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ | FragmentCatalog.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/DSViewer.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Subshape/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Subshape/ | SubshapeObjects.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Subshape/ | SubshapeAligner.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Subshape/ | SubshapeBuilder.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Subshape/ | BuilderUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/SimpleEnum/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/SimpleEnum/ | Enumerator.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Scaffolds/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Scaffolds/ | MurckoScaffold.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fraggle/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fraggle/ | FraggleSim.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AtomPairs/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AtomPairs/ | Sheridan.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AtomPairs/ | Pairs.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AtomPairs/ | Torsions.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/AtomPairs/ | Utils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | spingCanvas.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | aggCanvas.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | qtCanvas.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | IPythonConsole.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | canvasbase.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | MolDrawing.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | SimilarityMaps.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | cairoCanvas.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Draw/ | mplCanvas.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/FeatMaps/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/FeatMaps/ | FeatMaps.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/FeatMaps/ | FeatMapUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/FeatMaps/ | FeatMapPoint.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/FeatMaps/ | FeatMapParser.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/fmcs/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/fmcs/fmcs.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | Matcher.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | LazyGenerator.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | Gobbi_Pharm2D.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | Utils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | SigFactory.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm2D/ | Generate.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm3D/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm3D/ | Pharmacophore.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [..... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm3D/ | EmbedLib.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Pharm3D/ | ExcludedVolume.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/EState/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/EState/ | EState.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/EState/ | AtomTypes.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/EState/ | Fingerprinter.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/EState/ | EState_VSA.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolKey/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolKey/ | MolKey.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolKey/ | InchiInfo.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolDb/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolDb/ | FingerprintUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolDb/ | Loader_orig.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [...... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolDb/ | Loader_sa.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/MolDb/ | Loader.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | FingerprintMols.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | ClusterMols.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | MolSimilarity.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | DbFpSupplier.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Fingerprints/ | SimilarityScreener.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Features/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Features/ | ShowFeats.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Features/ | FeatDirUtilsRD.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Suppliers/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Suppliers/ | MolSupplier.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [....... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/Suppliers/ | DbMolSupplier.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | DescriptorUtilities.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | BulkTester.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | AlignDepict.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | SDFToCSV.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Chem/ChemUtils/ | TemplateExpand.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataManip/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataManip/Metric/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | HierarchyVis.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | VectCollection.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | LazySignature.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | BitEnsembleDb.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | TopNContainer.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | BitUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DataStructs/ | BitEnsemble.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/DbUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/DbInfo.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/DbModule.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/ | StorageUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/DbReport.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/ | DbConnection.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Dbase/ | DbResultSet.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/DistanceGeometry/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ForceField/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Geometry/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/MatOps.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/CompositeRun.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ | BuildComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ | ScreenComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ | AnalyzeComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/files.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/EnrichPlot.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ | GrowComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | Transforms.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.......... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | DataUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | Quantize.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/MLData.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/Stats.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | SplitData.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Data/ | FindQuantBounds.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ModelPackage/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ModelPackage/ | PackageUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/ModelPackage/ | Packager.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | ActFuncs.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | CrossValidate.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | Trainers.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [........... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | NetNode.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Neural/ | Network.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Composite/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Composite/ | BayesComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Composite/ | Composite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Composite/ | AdjustComposite.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | ClusterVis.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | Clusters.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | Resemblance.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | Standardize.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | Butina.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | ClusterUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Cluster/ | Murtagh.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/SLT/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/SLT/Risk.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/MLUtils/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/MLUtils/ | VoteImg.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ID3.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/Tree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | QuantTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | TreeVis.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | SigTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | CrossValidate.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | BuildSigTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | DecTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | BuildQuantTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | TreeUtils.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | PruneTree.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/DecTree/ | Forest.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Scoring/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Scoring/ | Scoring.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/InfoTheory/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/InfoTheory/ | entropy.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/InfoTheory/ | BitRank.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.............. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/InfoTheory/ | BitClusterer.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/NaiveBayes/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/NaiveBayes/ | CrossValidate.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/NaiveBayes/ | ClassificationModel.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/ | DistFunctions.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/ | KNNRegressionModel.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/KNNModel.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/ | KNNClassificationModel.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/KNN/ | CrossValidate.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Descriptors/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Descriptors/ | MoleculeDescriptors.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [............... +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Descriptors/ | CompoundDescriptors.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Descriptors/ | Parser.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/ML/Descriptors/ | Descriptors.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Numerics/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In rdBase: | No documentation available! | Error: Import failed: | ImportError: No module named rdBase | [................ +--------------------------------------------------------------------- | In RDConfig: | No documentation available! | Error: Import failed: | ImportError: No module named rdkit.RDPaths (line 39) | Error: Two of the specified items, 'rdBase' and 'RDConfig', have the same canonical name ("None"). This may mean that you specified two different files that both use the same module name. Ignoring the second item ('rdBase') [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/SimDivFilters/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/SimDivFilters/ | SimilarityPickers.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/Supply.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/Filter.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................ +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/Transform.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/Output.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/Node.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | __init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | DbMolSupply.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SDSupply.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SmartsMolFilter.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | DbPickleSupplier.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SmilesDupeFilter.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | demo.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SmartsRemover.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SmilesOutput.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/VLib/NodeLib/ | SmilesSupply.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [................. +--------------------------------------------------------------------- | In /<>/rdkit-201709.3+dfsg/rdkit/Avalon/__init__.py: | Import failed (but source code parsing was successful). | Error: ImportError: No module named rdBase (line 2) | [.................... Warning: No information available for rdkit.Chem.Descriptors.PropertyFunctor's base rdkit.Chem.rdMolDescriptors.PythonPropertyFunctor [.................... Warning: No information available for rdkit.Chem.FastSDMolSupplier.FastSDMolSupplier's base rdkit.Chem.SDMolSupplier [.................... Warning: No information available for rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint's base rdkit.Chem.ChemicalFeatures.FreeChemicalFeature [.................... Warning: rdkit.Chem.MolDb.Loader_sa.Compound's base declarative_base() is not a class [.................... Warning: No information available for rdkit.Chem.PropertyMol.PropertyMol's base rdkit.Chem.Mol [................................ Warning: No information available for rdkit.Chem.Descriptors.PropertyFunctor's base rdkit.Chem.rdMolDescriptors.PythonPropertyFunctor [................................ Warning: No information available for rdkit.Chem.FastSDMolSupplier.FastSDMolSupplier's base rdkit.Chem.SDMolSupplier [................................ Warning: No information available for rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint's base rdkit.Chem.ChemicalFeatures.FreeChemicalFeature [................................ Warning: rdkit.Chem.MolDb.Loader_sa.Compound's base declarative_base() is not a class [................................ Warning: No information available for rdkit.Chem.PropertyMol.PropertyMol's base rdkit.Chem.Mol [.........................................................................] (cd /<>/rdkit-201709.3+dfsg/Docs/Book; RDBASE=/<>/rdkit-201709.3+dfsg /usr/bin/make html) make[2]: Entering directory '/<>/rdkit-201709.3+dfsg/Docs/Book' mkdir -p _build/html/api mkdir -p _build/html/cppapi cp /<>/rdkit-201709.3+dfsg/rdkit/docs/* _build/html/api cp -r /<>/rdkit-201709.3+dfsg/Code/docs/* _build/html/cppapi sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.7.9 loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [html]: targets for 8 source files that are out of date updating environment: 8 added, 0 changed, 0 removed reading sources... [ 12%] Cartridge reading sources... [ 25%] Cookbook reading sources... [ 37%] GettingStartedInC++ reading sources... [ 50%] GettingStartedInPython reading sources... [ 62%] Install reading sources... [ 75%] Overview reading sources... [ 87%] RDKit_Book reading sources... [100%] index /usr/lib/python3/dist-packages/recommonmark/parser.py:280: UserWarning: Unsupported inline type Hardbreak warn("Unsupported inline type " + inline.t) /<>/rdkit-201709.3+dfsg/Docs/Book/GettingStartedInPython.rst:2332: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... /<>/rdkit-201709.3+dfsg/Docs/Book/GettingStartedInC++.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 12%] Cartridge writing output... [ 25%] Cookbook writing output... [ 37%] GettingStartedInC++ writing output... [ 50%] GettingStartedInPython writing output... [ 62%] Install writing output... [ 75%] Overview writing output... [ 87%] RDKit_Book writing output... [100%] index generating indices... genindex writing additional pages... search copying images... [ 4%] images/indole1.png copying images... [ 8%] images/similarity_map_rf.png copying images... [ 12%] images/picture_1.png copying images... [ 16%] images/picture_0.png copying images... [ 20%] images/picture_3.png copying images... [ 25%] images/picture_2.png copying images... [ 29%] images/picture_4.png copying images... [ 33%] images/cdk2_mol1.png copying images... [ 37%] images/cdk2_mol2.png copying images... [ 41%] images/cdk2_molgrid.png copying images... [ 45%] images/cdk2_molgrid_aligned.png copying images... [ 50%] images/similarity_map_fp1.png copying images... [ 54%] images/similarity_map_fp2.png copying images... [ 58%] images/similarity_map_fp3.png copying images... [ 62%] images/similarity_map_charges.png copying images... [ 66%] images/similarity_map_crippen.png copying images... [ 70%] images/picture_6.png copying images... [ 75%] images/picture_5.png copying images... [ 79%] images/picture_9.png copying images... [ 83%] images/picture_8.png copying images... [ 87%] images/picture_7.png copying images... [ 91%] images/picture_10.png copying images... [ 95%] images/picture_11.png copying images... [100%] images/picture_10.jpg copying static files... WARNING: html_static_path entry '/<>/rdkit-201709.3+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, 3 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/<>/rdkit-201709.3+dfsg/Docs/Book' (cd /<>/rdkit-201709.3+dfsg/Docs/Book; RDBASE=/<>/rdkit-201709.3+dfsg /usr/bin/make latexpdf) make[2]: Entering directory '/<>/rdkit-201709.3+dfsg/Docs/Book' mkdir -p _build/html/api mkdir -p _build/html/cppapi cp /<>/rdkit-201709.3+dfsg/rdkit/docs/* _build/html/api cp -r /<>/rdkit-201709.3+dfsg/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v1.7.9 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: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing RDKit.tex...index Overview Install GettingStartedInPython RDKit_Book Cookbook Cartridge resolving references... writing... done copying images... [ 4%] images/picture_1.png copying images... [ 8%] images/picture_0.png copying images... [ 12%] images/picture_3.png copying images... [ 16%] images/picture_2.png copying images... [ 20%] images/picture_4.png copying images... [ 25%] images/cdk2_mol1.png copying images... [ 29%] images/cdk2_mol2.png copying images... [ 33%] images/cdk2_molgrid.png copying images... [ 37%] images/cdk2_molgrid_aligned.png copying images... [ 41%] images/similarity_map_fp1.png copying images... [ 45%] images/similarity_map_fp2.png copying images... [ 50%] images/similarity_map_fp3.png copying images... [ 54%] images/similarity_map_charges.png copying images... [ 58%] images/similarity_map_crippen.png copying images... [ 62%] images/picture_6.png copying images... [ 66%] images/picture_5.png copying images... [ 70%] images/picture_9.png copying images... [ 75%] images/picture_8.png copying images... [ 79%] images/picture_7.png copying images... [ 83%] images/picture_10.png copying images... [ 87%] images/picture_11.png copying images... [ 91%] images/picture_10.jpg copying images... [ 95%] images/indole1.png copying images... [100%] images/similarity_map_rf.png copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). Running LaTeX files through pdflatex... make -C _build/latex all-pdf make[3]: Entering directory '/<>/rdkit-201709.3+dfsg/Docs/Book/_build/latex' latexmk -pdf -dvi- -ps- 'RDKit.tex' Latexmk: This is Latexmk, John Collins, 21 September 2018, version: 4.60. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "RDKit.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./RDKit.tex LaTeX2e <2018-04-01> patch level 5 (./sphinxmanual.cls Document Class: sphinxmanual 2017/03/26 v1.6 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 103--104 []\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 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 238. LaTeX Warning: Hyper reference `Overview:footnote2' on page 2 undefined on inpu t line 247. [2] LaTeX Warning: Hyper reference `Overview:footnote6' on page 3 undefined on inpu t line 271. LaTeX Warning: Hyper reference `Overview:footnote7' on page 3 undefined on inpu t line 276. LaTeX Warning: Hyper reference `Overview:footnote9' on page 3 undefined on inpu t line 298. LaTeX Warning: Hyper reference `Overview:footnote1' on page 3 undefined on inpu t line 304. 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Underfull \hbox (badness 6268) in paragraph at lines 449--450 \T1/ptm/m/n/10 Dimensionality of Molecules^^Q \T1/ptm/m/it/10 Jour-nal of Chem- i-cal In-for-ma-tion and Mod-el-ing \T1/ptm/b/n/10 52 \T1/ptm/m/n/10 2516-2525 (2012). [4] [5] [6] Chapter 2. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 757--758 []\T1/ptm/m/n/10 Here things are more dif-fi-cult. Check this wiki page for in- for-ma-tion: [10] Underfull \hbox (badness 5008) in paragraph at lines 823--824 []\T1/ptm/m/n/10 If not us-ing the python wrap-pers: \T1/pcr/m/n/10 ./bootstrap .sh --with-libraries=regex,thread, [11] Underfull \hbox (badness 10000) in paragraph at lines 954--955 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \hbox (badness 10000) in paragraph at lines 1052--1053 []\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/ [13] Underfull \hbox (badness 10000) in paragraph at lines 1066--1067 []\T1/ptm/m/n/10 This can be solved by us-ing cmake ver-sion 2.8.3 (or more re- cent) and pro-vid-ing the \T1/pcr/m/n/10 -D [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 []\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 1237--1239 \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 1237--1239 \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 1237--1239 \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 1237--1239 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1247--1248 []\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 1253--1254 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [16] [17] [18] Chapter 3. 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No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [115] (./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}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on RDKit.pdf (119 pages, 1552972 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. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'RDKit.aux' 'RDKit.ind' 'RDKit.out' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "RDKit.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 103--104 []\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 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 238. LaTeX Warning: Hyper reference `Overview:footnote2' on page 2 undefined on inpu t line 247. [2] LaTeX Warning: Hyper reference `Overview:footnote6' on page 3 undefined on inpu t line 271. LaTeX Warning: Hyper reference `Overview:footnote7' on page 3 undefined on inpu t line 276. LaTeX Warning: Hyper reference `Overview:footnote9' on page 3 undefined on inpu t line 298. LaTeX Warning: Hyper reference `Overview:footnote1' on page 3 undefined on inpu t line 304. LaTeX Warning: Hyper reference `Overview:footnote3' on page 3 undefined on inpu t line 316. LaTeX Warning: Hyper reference `Overview:footnote1' on page 3 undefined on inpu t line 316. LaTeX Warning: Hyper reference `Overview:footnote4' on page 3 undefined on inpu t line 319. LaTeX Warning: Hyper reference `Overview:footnote5' on page 3 undefined on inpu t line 331. LaTeX Warning: Hyper reference `Overview:footnote8' on page 3 undefined on inpu t line 336. LaTeX Warning: Hyper reference `Overview:footnote1' on page 3 undefined on inpu t line 353. [3] Underfull \hbox (badness 10000) in paragraph at lines 427--428 \T1/ptm/m/n/10 dic-tion with Flu-o-rine Fin-ger-print De-scrip-tor^^Q \T1/ptm/m /it/10 J. of Flu-o-rine Chem-istry \T1/ptm/b/n/10 131 \T1/ptm/m/n/10 (2010) 570 -577. Underfull \hbox (badness 6268) in paragraph at lines 449--450 \T1/ptm/m/n/10 Dimensionality of Molecules^^Q \T1/ptm/m/it/10 Jour-nal of Chem- i-cal In-for-ma-tion and Mod-el-ing \T1/ptm/b/n/10 52 \T1/ptm/m/n/10 2516-2525 (2012). [4] [5] [6] Chapter 2. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 757--758 []\T1/ptm/m/n/10 Here things are more dif-fi-cult. Check this wiki page for in- for-ma-tion: [10] Underfull \hbox (badness 5008) in paragraph at lines 823--824 []\T1/ptm/m/n/10 If not us-ing the python wrap-pers: \T1/pcr/m/n/10 ./bootstrap .sh --with-libraries=regex,thread, [11] Underfull \hbox (badness 10000) in paragraph at lines 954--955 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \hbox (badness 10000) in paragraph at lines 1052--1053 []\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/ [13] Underfull \hbox (badness 10000) in paragraph at lines 1066--1067 []\T1/ptm/m/n/10 This can be solved by us-ing cmake ver-sion 2.8.3 (or more re- cent) and pro-vid-ing the \T1/pcr/m/n/10 -D [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 []\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 1237--1239 \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 1237--1239 \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 1237--1239 \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 1237--1239 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1247--1248 []\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 1253--1254 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [16] [17] [18] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 1348--1349 []\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 [19] [20] [21] [22] [23] [24] [25] [26] [27 <./picture_1.png (PNG copy)> <./pic ture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1929--1934 []\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. [28 <./picture_2.png> <./picture_4.png>] [29] [30] [31 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [32 <./cdk2_molgrid.png>] [33 <./cdk2_molgrid_aligned.png (PNG cop y)>] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45 <./similarity_m ap_fp1.png>] [46 <./similarity_map_fp2.png>] [47 <./similarity_map_fp3.png>] [48] [49 <./similarity_map_charges.png>] [50 <./similarity_map_crippen.png>] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6792) in paragraph at lines 3870--3873 []\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 4198--4202 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Underfull \hbox (badness 10000) in paragraph at lines 4208--4212 []|\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 4276--4277 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}Rings| Overfull \hbox (91.89552pt too wide) in paragraph at lines 4281--4282 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}{Hetero,Carbo}cycles| Underfull \hbox (badness 10000) in paragraph at lines 4310--4313 []|\T1/ptm/m/n/10 Number of bridge-head atoms Underfull \hbox (badness 10000) in paragraph at lines 4336--4339 \T1/ptm/m/n/10 tions [][]$http : / / www . chemcomp . com / Underfull \hbox (badness 10000) in paragraph at lines 4345--4349 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . Underfull \hbox (badness 10000) in paragraph at lines 4355--4359 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . 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[67 <./picture_9.png (PNG copy)>] [68 <./picture_8.png> <./picture_7.png (PNG c opy)>] [69 <./picture_10.png> <./picture_11.png>] [70] [71] [72] [73] [74] [75] [76 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 5526 [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [79] [80] Chapter 5. [81] [82 <./indole1.png>] [83] [84] [85] Overfull \vbox (1.52577pt too high) detected at line 6195 [86] [87] [88] Overfull \vbox (1.13905pt too high) detected at line 6383 [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 6418--6419 []\T1/ptm/m/n/10 IPython note-book: [][]$http : / / nbviewer . ipython . org / gist / greglandrum / 8351725$[][] [][]$https : / / gist . github . com / gregla ndrum / [91 <./similarity_map_rf.png>] [92] [93] Underfull \vbox (badness 10000) detected at line 6648 Overfull \vbox (2.68169pt too high) detected at line 6648 [94] [95] [96] Chapter 6. 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(./RDKit.ind) [115] (./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}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on RDKit.pdf (121 pages, 1578829 bytes). Transcript written on RDKit.log. 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LaTeX Warning: Label `Cartridge: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]) [4] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 103--104 []\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 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 191. LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 238. LaTeX Warning: Hyper reference `Overview:footnote2' on page 2 undefined on inpu t line 247. [2] LaTeX Warning: Hyper reference `Overview:footnote6' on page 3 undefined on inpu t line 271. LaTeX Warning: Hyper reference `Overview:footnote7' on page 3 undefined on inpu t line 276. LaTeX Warning: Hyper reference `Overview:footnote9' on page 3 undefined on inpu t line 298. LaTeX Warning: Hyper reference `Overview:footnote1' on page 3 undefined on inpu t line 304. 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Underfull \hbox (badness 6268) in paragraph at lines 449--450 \T1/ptm/m/n/10 Dimensionality of Molecules^^Q \T1/ptm/m/it/10 Jour-nal of Chem- i-cal In-for-ma-tion and Mod-el-ing \T1/ptm/b/n/10 52 \T1/ptm/m/n/10 2516-2525 (2012). [4] [5] [6] Chapter 2. [7] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 757--758 []\T1/ptm/m/n/10 Here things are more dif-fi-cult. Check this wiki page for in- for-ma-tion: [10] Underfull \hbox (badness 5008) in paragraph at lines 823--824 []\T1/ptm/m/n/10 If not us-ing the python wrap-pers: \T1/pcr/m/n/10 ./bootstrap .sh --with-libraries=regex,thread, [11] Underfull \hbox (badness 10000) in paragraph at lines 954--955 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \hbox (badness 10000) in paragraph at lines 1052--1053 []\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/ [13] Underfull \hbox (badness 10000) in paragraph at lines 1066--1067 []\T1/ptm/m/n/10 This can be solved by us-ing cmake ver-sion 2.8.3 (or more re- cent) and pro-vid-ing the \T1/pcr/m/n/10 -D [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 []\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 1237--1239 \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 1237--1239 \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 1237--1239 \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 1237--1239 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1237--1239 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" Underfull \hbox (badness 10000) in paragraph at lines 1247--1248 []\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 1253--1254 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [16] [17] [18] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 1348--1349 []\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 [19] [20] [21] [22] [23] [24] [25] [26] [27 <./picture_1.png (PNG copy)> <./pic ture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1929--1934 []\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. [28 <./picture_2.png> <./picture_4.png>] [29] [30] [31 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [32 <./cdk2_molgrid.png>] [33 <./cdk2_molgrid_aligned.png (PNG cop y)>] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45 <./similarity_m ap_fp1.png>] [46 <./similarity_map_fp2.png>] [47 <./similarity_map_fp3.png>] [48] [49 <./similarity_map_charges.png>] [50 <./similarity_map_crippen.png>] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6792) in paragraph at lines 3870--3873 []\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 4198--4202 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Underfull \hbox (badness 10000) in paragraph at lines 4208--4212 []|\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 4276--4277 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}Rings| Overfull \hbox (91.89552pt too wide) in paragraph at lines 4281--4282 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}{Hetero,Carbo}cycles| Underfull \hbox (badness 10000) in paragraph at lines 4310--4313 []|\T1/ptm/m/n/10 Number of bridge-head atoms Underfull \hbox (badness 10000) in paragraph at lines 4336--4339 \T1/ptm/m/n/10 tions [][]$http : / / www . chemcomp . com / Underfull \hbox (badness 10000) in paragraph at lines 4345--4349 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . 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[67 <./picture_9.png (PNG copy)>] [68 <./picture_8.png> <./picture_7.png (PNG c opy)>] [69 <./picture_10.png> <./picture_11.png>] [70] [71] [72] [73] [74] [75] [76 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 5526 [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 5755--5755 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [79] [80] Chapter 5. [81] [82 <./indole1.png>] [83] [84] [85] Overfull \vbox (1.52577pt too high) detected at line 6195 [86] [87] [88] Overfull \vbox (1.13905pt too high) detected at line 6383 [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 6418--6419 []\T1/ptm/m/n/10 IPython note-book: [][]$http : / / nbviewer . ipython . org / gist / greglandrum / 8351725$[][] [][]$https : / / gist . github . com / gregla ndrum / [91 <./similarity_map_rf.png>] [92] [93] Underfull \vbox (badness 10000) detected at line 6648 Overfull \vbox (2.68169pt too high) detected at line 6648 [94] [95] [96] Chapter 6. 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(10.4835pt too high) detected at line 7212 [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] Chapter 7. (./RDKit.ind) [115] (./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}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on RDKit.pdf (121 pages, 1578829 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 `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' 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Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/<>/rdkit-201709.3+dfsg/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/<>/rdkit-201709.3+dfsg/Docs/Book' make[1]: Leaving directory '/<>/rdkit-201709.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/rdkit-201709.3+dfsg' cp -r rdkit obj-*/ find /<>/rdkit-201709.3+dfsg -name rdchem.so /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/rdchem.so #export RDBASE=/<>/rdkit-201709.3+dfsg PYTHONPATH=/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/ LD_LIBRARY_PATH="/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf//lib:" RDBASE=/<>/rdkit-201709.3+dfsg PYTHONPATH=/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/:/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf//rdkit/Chem/ LD_LIBRARY_PATH="/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf//lib:" dh_auto_test cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=-j4 make[2]: Entering directory '/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process -j4 Test project /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf Start 1: testDict Start 2: testRDValue Start 3: testDataStructs Start 4: testFPB 1/123 Test #2: testRDValue ........................ Passed 0.01 sec Start 5: testMultiFPB 2/123 Test #3: testDataStructs .................... Passed 0.01 sec Start 6: pyBV 3/123 Test #4: testFPB ............................ Passed 0.01 sec Start 7: pyDiscreteValueVect 4/123 Test #5: testMultiFPB ....................... Passed 0.03 sec Start 8: pySparseIntVect 5/123 Test #7: pyDiscreteValueVect ................ Passed 0.18 sec Start 9: pyFPB 6/123 Test #8: pySparseIntVect .................... Passed 0.17 sec Start 10: testTransforms 7/123 Test #10: testTransforms ..................... Passed 0.01 sec Start 11: testGrid 8/123 Test #11: testGrid ........................... Passed 0.06 sec Start 12: testPyGeometry 9/123 Test #9: pyFPB .............................. Passed 0.17 sec Start 13: testMatrices 10/123 Test #13: testMatrices ....................... Passed 0.01 sec Start 14: testAlignment 11/123 Test #14: testAlignment ...................... Passed 0.01 sec Start 15: pyAlignment 12/123 Test #12: testPyGeometry ..................... Passed 0.23 sec Start 16: testOptimizer 13/123 Test #16: testOptimizer ...................... Passed 0.01 sec Start 17: testUFFForceField 14/123 Test #15: pyAlignment ........................ Passed 0.17 sec Start 18: testMMFFForceField 15/123 Test #17: testUFFForceField .................. Passed 0.16 sec Start 19: pyForceFieldConstraints 16/123 Test #6: pyBV ............................... Passed 1.30 sec Start 20: testDistGeom 17/123 Test #20: testDistGeom ....................... Passed 0.01 sec Start 21: pyDistGeom 18/123 Test #21: pyDistGeom ......................... Passed 0.16 sec Start 22: graphmolTest1 19/123 Test #19: pyForceFieldConstraints ............ Passed 0.97 sec Start 23: graphmolcpTest 20/123 Test #23: graphmolcpTest ..................... Passed 0.03 sec Start 24: graphmolqueryTest 21/123 Test #22: graphmolTest1 ...................... Passed 0.22 sec Start 25: graphmolMolOpsTest 22/123 Test #24: graphmolqueryTest .................. Passed 0.04 sec Start 26: graphmoltestCanon 23/123 Test #26: graphmoltestCanon .................. Passed 0.01 sec Start 27: graphmoltestChirality 24/123 Test #27: graphmoltestChirality .............. Passed 0.07 sec Start 28: graphmoltestPickler 25/123 Test #28: graphmoltestPickler ................ Passed 0.44 sec Start 29: graphmoltestPicklerGlobalSetting 26/123 Test #29: graphmoltestPicklerGlobalSetting ... Passed 0.04 sec Start 30: graphmolIterTest 27/123 Test #30: graphmolIterTest ................... Passed 0.03 sec Start 31: hanoiTest 28/123 Test #1: testDict ........................... Passed 2.48 sec Start 32: graphmolMemTest1 29/123 Test #32: graphmolMemTest1 ................... Passed 0.01 sec Start 33: resMolSupplierTest 30/123 Test #33: resMolSupplierTest ................. Passed 1.54 sec Start 34: molBundleTest 31/123 Test #34: molBundleTest ...................... Passed 0.04 sec Start 35: testDepictor 32/123 Test #35: testDepictor ....................... Passed 0.62 sec Start 36: pyDepictor 33/123 Test #36: pyDepictor ......................... Passed 0.59 sec Start 37: smiTest1 34/123 Test #37: smiTest1 ........................... Passed 0.35 sec Start 38: cxsmilesTest 35/123 Test #38: cxsmilesTest ....................... Passed 0.03 sec Start 39: smaTest1 36/123 Test #25: graphmolMolOpsTest ................. Passed 4.10 sec Start 40: fileParsersTest1 37/123 Test #39: smaTest1 ........................... Passed 1.77 sec Start 41: testMolSupplier 38/123 Test #41: testMolSupplier .................... Passed 0.28 sec Start 42: testMolWriter 39/123 Test #42: testMolWriter ...................... Passed 0.47 sec Start 43: testTplParser 40/123 Test #43: testTplParser ...................... Passed 0.04 sec Start 44: testMol2ToMol 41/123 Test #44: testMol2ToMol ...................... Passed 0.05 sec Start 45: testSequence 42/123 Test #45: testSequence ....................... Passed 0.09 sec Start 46: testSubstructMatch 43/123 Test #46: testSubstructMatch ................. Passed 1.09 sec Start 47: testReaction 44/123 Test #47: testReaction ....................... Passed 0.38 sec Start 48: testReactionFingerprints 45/123 Test #48: testReactionFingerprints ........... Passed 0.06 sec Start 49: testEnumeration 46/123 Test #40: fileParsersTest1 ................... Passed 23.91 sec Start 50: pyChemReactions 47/123 Test #50: pyChemReactions .................... Passed 0.39 sec Start 51: pyChemReactionEnumerations 48/123 Test #18: testMMFFForceField ................. Passed 32.76 sec Start 52: pyChemReactionSanitize 49/123 Test #52: pyChemReactionSanitize ............. Passed 0.29 sec Start 53: testChemTransforms 50/123 Test #53: testChemTransforms ................. Passed 0.13 sec Start 54: testSubgraphs1 51/123 Test #54: testSubgraphs1 ..................... Passed 0.48 sec Start 55: testSubgraphs2 52/123 Test #55: testSubgraphs2 ..................... Passed 0.03 sec Start 56: filterCatalogTest 53/123 Test #56: filterCatalogTest .................. Passed 0.20 sec Start 57: pyFilterCatalog 54/123 Test #57: pyFilterCatalog .................... Passed 2.76 sec Start 58: testFragCatalog 55/123 Test #58: testFragCatalog .................... Passed 1.33 sec Start 59: pyFragCatalog 56/123 Test #59: pyFragCatalog ...................... Passed 0.31 sec Start 60: testDescriptors 57/123 Test #51: pyChemReactionEnumerations ......... Passed 8.79 sec Start 61: testAUTOCORR2D 58/123 Test #61: testAUTOCORR2D ..................... Passed 0.73 sec Start 62: pyMolDescriptors 59/123 Test #62: pyMolDescriptors ................... Passed 0.73 sec Start 63: pyMolDescriptors3D 60/123 Test #63: pyMolDescriptors3D ................. Passed 0.50 sec Start 64: testFingerprints 61/123 Test #60: testDescriptors .................... Passed 12.22 sec Start 65: testPartialCharges 62/123 Test #65: testPartialCharges ................. Passed 0.06 sec Start 66: pyPartialCharges 63/123 Test #66: pyPartialCharges ................... Passed 0.68 sec Start 67: testMolTransforms 64/123 Test #67: testMolTransforms .................. Passed 0.09 sec Start 68: pyMolTransforms 65/123 Test #68: pyMolTransforms .................... Passed 0.49 sec Start 69: testMMFFForceFieldHelpers 66/123 Test #31: hanoiTest .......................... Passed 55.00 sec Start 70: testUFFForceFieldHelpers 67/123 Test #64: testFingerprints ................... Passed 26.46 sec Start 71: testCrystalForceField 68/123 Test #71: testCrystalForceField .............. Passed 0.09 sec Start 72: pyForceFieldHelpers 69/123 Test #72: pyForceFieldHelpers ................ Passed 0.45 sec Start 73: testDistGeomHelpers 70/123 Test #69: testMMFFForceFieldHelpers .......... Passed 59.24 sec Start 74: pyDistGeom 71/123 Test #70: testUFFForceFieldHelpers ........... Passed 63.16 sec Start 75: testMolAlign 72/123 Test #74: pyDistGeom ......................... Passed 45.89 sec Start 76: pyMolAlign 73/123 Test #76: pyMolAlign ......................... Passed 27.76 sec Start 77: testFeatures 74/123 Test #77: testFeatures ....................... Passed 0.06 sec Start 78: pyChemicalFeatures 75/123 Test #78: pyChemicalFeatures ................. Passed 0.28 sec Start 79: testShapeHelpers 76/123 Test #79: testShapeHelpers ................... Passed 0.05 sec Start 80: pyShapeHelpers 77/123 Test #80: pyShapeHelpers ..................... Passed 0.35 sec Start 81: testMolCatalog 78/123 Test #81: testMolCatalog ..................... Passed 0.03 sec Start 82: pyMolCatalog 79/123 Test #82: pyMolCatalog ....................... Passed 0.22 sec Start 83: moldraw2DTest1 80/123 Test #83: moldraw2DTest1 ..................... Passed 3.48 sec Start 84: moldraw2DRxnTest1 81/123 Test #84: moldraw2DRxnTest1 .................. Passed 0.07 sec Start 85: pyMolDraw2D 82/123 Test #85: pyMolDraw2D ........................ Passed 0.31 sec Start 86: testFMCS 83/123 Test #86: testFMCS ........................... Passed 1.09 sec Start 87: pyFMCS 84/123 Test #87: pyFMCS ............................. Passed 1.81 sec Start 88: FMCStest 85/123 Test #88: FMCStest ........................... Passed 0.07 sec Start 89: testMolHash 86/123 Test #89: testMolHash ........................ Passed 0.26 sec Start 90: pyMolHash 87/123 Test #90: pyMolHash .......................... Passed 0.20 sec Start 91: testMMPA 88/123 Test #91: testMMPA ........................... Passed 0.19 sec Start 92: pyMMPA 89/123 Test #92: pyMMPA ............................. Passed 2.72 sec Start 93: testStructChecker 90/123 Test #93: testStructChecker .................. Passed 0.13 sec Start 94: pyStructChecker 91/123 Test #94: pyStructChecker .................... Passed 0.23 sec Start 95: testReducedGraphs 92/123 Test #95: testReducedGraphs .................. Passed 0.10 sec Start 96: pyReducedGraphs 93/123 Test #96: pyReducedGraphs .................... Passed 0.22 sec Start 97: trajectoryTest 94/123 Test #97: trajectoryTest ..................... Passed 1.02 sec Start 98: substructLibraryTest 95/123 Test #98: substructLibraryTest ............... Passed 0.97 sec Start 99: pySubstructLibrary 96/123 Test #99: pySubstructLibrary ................. Passed 2.72 sec Start 100: testRGroupDecomp 97/123 Test #100: testRGroupDecomp ................... Passed 0.33 sec Start 101: pyRGroupDecomposition 98/123 Test #101: pyRGroupDecomposition .............. Passed 0.43 sec Start 102: testSLNParse 99/123 Test #102: testSLNParse ....................... Passed 0.06 sec Start 103: pySLNParse 100/123 Test #103: pySLNParse ......................... Passed 0.23 sec Start 104: pyGraphMolWrap 101/123 Test #73: testDistGeomHelpers ................ Passed 150.14 sec Start 105: pyTestConformerWrap 102/123 Test #105: pyTestConformerWrap ................ Passed 0.45 sec Start 106: pyTestTrajectory 103/123 Test #106: pyTestTrajectory ................... Passed 1.30 sec Start 107: pyTestThreads 104/123 Test #107: pyTestThreads ...................... Passed 0.34 sec Start 108: testQuery 105/123 Test #108: testQuery .......................... Passed 0.01 sec Start 109: testMatCalc 106/123 Test #109: testMatCalc ........................ Passed 0.01 sec Start 110: pyMatCalc 107/123 Test #110: pyMatCalc .......................... Passed 1.17 sec Start 111: testSimDivPickers 108/123 Test #111: testSimDivPickers .................. Passed 0.01 sec Start 112: pySimDivPickers 109/123 Test #104: pyGraphMolWrap ..................... Passed 18.67 sec Start 113: pyRanker 110/123 Test #113: pyRanker ........................... Passed 0.21 sec Start 114: testChemicalFeatures 111/123 Test #114: testChemicalFeatures ............... Passed 0.01 sec Start 115: pyFeatures 112/123 Test #112: pySimDivPickers .................... Passed 0.56 sec Start 116: pythonTestDbCLI 113/123 Test #115: pyFeatures ......................... Passed 0.21 sec Start 117: pythonTestDirML 114/123 Test #117: pythonTestDirML .................... Passed 18.10 sec Start 118: pythonTestDirDataStructs 115/123 Test #118: pythonTestDirDataStructs ........... Passed 1.82 sec Start 119: pythonTestDirDbase 116/123 Test #119: pythonTestDirDbase ................. Passed 2.19 sec Start 120: pythonTestDirSimDivFilters 117/123 Test #120: pythonTestDirSimDivFilters ......... Passed 0.66 sec Start 121: pythonTestDirVLib 118/123 Test #121: pythonTestDirVLib .................. Passed 1.09 sec Start 122: pythonTestDirChem 119/123 Test #116: pythonTestDbCLI .................... Passed 36.24 sec Start 123: pythonTestSping 120/123 Test #123: pythonTestSping .................... Passed 1.18 sec 121/123 Test #75: testMolAlign ....................... Passed 217.94 sec 122/123 Test #122: pythonTestDirChem ..................***Failed 135.50 sec .... ---------------------------------------------------------------------- Ran 4 tests in 0.181s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.147s OK ....[08:54:42] **** Pre-condition Violation valence not defined for atoms not associated with molecules Violation occurred on line 267 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/Atom.cpp Failed Expression: dp_mol **** . ---------------------------------------------------------------------- Ran 5 tests in 0.031s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.043s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.027s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.065s OK .....s.................ss ---------------------------------------------------------------------- Ran 25 tests in 0.440s OK (skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 0.589s OK (skipped=1) ................................... ---------------------------------------------------------------------- Ran 35 tests in 1.569s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.033s OK . ---------------------------------------------------------------------- Ran 1 test in 0.021s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.063s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.107s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 2.243s OK (skipped=4) .......F...[08:55:23] WARNING: More than one matching pattern found - picking one [08:55:24] WARNING: More than one matching pattern found - picking one .[08:55:24] 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 14 tests in 32.821s FAILED (failures=1) ........ ---------------------------------------------------------------------- Ran 8 tests in 0.215s OK ........... ---------------------------------------------------------------------- Ran 11 tests in 7.546s OK .... ---------------------------------------------------------------------- Ran 4 tests in 2.953s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.732s OK ...............s/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:391: 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))]) /<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:391: 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))]) ./<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:410: 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 5.682s OK (skipped=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.000s 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/<>/rdkit-201709.3+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 .............[08:55:59] WARNING: More than one matching pattern found - picking one [08:55:59] 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 2226, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers File "/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/EnumerateStereoisomers.py", line 97, in EnumerateStereoisomers ---------------------------------------------------------------------- File "/<>/rdkit-201709.3+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/EnumerateStereoisomers.py", line 189, 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 23 tests in 15.363s FAILED (failures=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.159s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 2.265s OK (skipped=1) .................. ---------------------------------------------------------------------- Ran 18 tests in 1.588s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.225s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.055s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.040s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.030s OK . ---------------------------------------------------------------------- Ran 1 test in 0.167s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.002s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.005s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.003s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.008s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.026s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.033s OK .... ---------------------------------------------------------------------- Ran 4 tests in 8.312s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.094s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.006s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.159s OK ..................... ---------------------------------------------------------------------- Ran 21 tests in 11.286s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...[08:56:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 37 in file /<>/rdkit-201709.3+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp Failed Expression: dp_mol->getNumConformers() **** . ---------------------------------------------------------------------- Ran 4 tests in 0.041s OK .. ---------------------------------------------------------------------- Ran 2 tests in 19.943s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.181s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.024s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.037s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.667s OK ssssss...s..... ---------------------------------------------------------------------- Ran 15 tests in 0.250s OK (skipped=7) s ---------------------------------------------------------------------- Ran 1 test in 0.000s OK (skipped=1) .......... ---------------------------------------------------------------------- Ran 10 tests in 1.082s OK ..[08:56:55] reaction has no reactants [08:56:55] reaction has no products [08:56:55] initialization failed [08:56:55] reaction has no reactants [08:56:55] reaction has no products . ---------------------------------------------------------------------- Ran 3 tests in 0.047s OK !!! TEST FAILURE: python UnitTestMol3D.py {} !!! TEST FAILURE: python UnitTestDocTestsChem.py {} E: Build killed with signal TERM after 720 minutes of inactivity -------------------------------------------------------------------------------- Build finished at 2018-10-21T20:56:56Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: binary Build-Space: 1645492 Build-Time: 45320 Distribution: sid Fail-Stage: build Host Architecture: armhf Install-Time: 310 Job: /chroot/rebuildd/build-rdkit/rdkit_201709.3+dfsg-1.dsc Machine Architecture: arm64 Package: rdkit Package-Time: 45689 Source-Version: 201709.3+dfsg-1 Space: 1645492 Status: attempted Version: 201709.3+dfsg-1 -------------------------------------------------------------------------------- Finished at 2018-10-21T20:56:56Z Build needed 12:41:29, 1645492k disk space E: Build failure (dpkg-buildpackage died)