DC-Build-Header: rdkit 201403-1 / 2015-03-26 10:38:20 +0000 DC-Task: source:rdkit version:201403-1 architecture:any chroot:unstable esttime:5168 logfile:/tmp/rdkit_201403-1_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang rdkit_201403-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-9-76.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ rdkit 201403-1 (amd64) 26 Mar 2015 10:38 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: rdkit Version: 201403-1 Source Version: 201403-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/rdkit-CxP0Ss/rdkit-201403' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/rdkit-CxP0Ss' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-94cbf51d-9f77-48e3-93d9-1ea603e96b2f' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [257 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2015-03-25-1448.37.pdiff [3021 B] Get:6 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [5545 B] Get:7 http://localhost:9999 unstable/main 2015-03-26-0248.39.pdiff [3389 B] Get:8 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [2242 B] Get:9 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [2242 B] Get:10 http://localhost:9999 unstable/main amd64 2015-03-25-1448.37.pdiff [4095 B] Get:11 http://localhost:9999 unstable/main amd64 2015-03-25-2049.47.pdiff [4595 B] Get:12 http://localhost:9999 unstable/main amd64 2015-03-26-0248.39.pdiff [3173 B] Get:13 http://localhost:9999 unstable/main amd64 2015-03-26-0844.35.pdiff [1129 B] Get:14 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Get:15 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [464 B] Get:16 http://localhost:9999 unstable/main amd64 2015-03-26-0844.35.pdiff [1129 B] Get:17 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [464 B] Fetched 310 kB in 4s (69.4 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'rdkit' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debichem/unstable/rdkit/ Need to get 23.7 MB of source archives. Get:1 http://localhost:9999/debian/ unstable/main rdkit 201403-1 (dsc) [2300 B] Get:2 http://localhost:9999/debian/ unstable/main rdkit 201403-1 (tar) [23.7 MB] Get:3 http://localhost:9999/debian/ unstable/main rdkit 201403-1 (diff) [6568 B] Fetched 23.7 MB in 12s (1937 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/clang ────────── + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.6 + echo 'Install of clang-3.6' Install of clang-3.6 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (13.6 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.6 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.6-doc Recommended packages: llvm-3.6-dev python The following NEW packages will be installed: clang-3.6 libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After this operation, 153 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2+b2 [20.1 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.6 amd64 1:3.6-2 [8137 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.2-10 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.2-10 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.6 amd64 1:3.6-2 [3839 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.6-dev amd64 1:3.6-2 [706 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.6 amd64 1:3.6-2 [25.8 MB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 39.2 MB in 0s (42.7 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11980 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+b2) ... Selecting previously unselected package libllvm3.6:amd64. Preparing to unpack .../libllvm3.6_1%3a3.6-2_amd64.deb ... Unpacking libllvm3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.2-10_amd64.deb ... Unpacking libobjc4:amd64 (4.9.2-10) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.2-10_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.2-10) ... Selecting previously unselected package libclang1-3.6:amd64. Preparing to unpack .../libclang1-3.6_1%3a3.6-2_amd64.deb ... Unpacking libclang1-3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libclang-common-3.6-dev. Preparing to unpack .../libclang-common-3.6-dev_1%3a3.6-2_amd64.deb ... Unpacking libclang-common-3.6-dev (1:3.6-2) ... Selecting previously unselected package clang-3.6. Preparing to unpack .../clang-3.6_1%3a3.6-2_amd64.deb ... Unpacking clang-3.6 (1:3.6-2) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2+b2) ... Setting up libllvm3.6:amd64 (1:3.6-2) ... Setting up libobjc4:amd64 (4.9.2-10) ... Setting up libobjc-4.9-dev:amd64 (4.9.2-10) ... Setting up libclang1-3.6:amd64 (1:3.6-2) ... Setting up libclang-common-3.6-dev (1:3.6-2) ... Setting up clang-3.6 (1:3.6-2) ... Processing triggers for libc-bin (2.19-17) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.6 g++-4.6 + ln -s clang-3.6 gcc-4.6 + ln -s clang-3.6 cpp-4.6 + ln -s clang-3.6 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.6 g++-4.7 + ln -s clang-3.6 gcc-4.7 + ln -s clang-3.6 cpp-4.7 + ln -s clang-3.6 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.6 g++-4.8 + ln -s clang-3.6 gcc-4.8 + ln -s clang-3.6 cpp-4.8 + ln -s clang-3.6 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.6 g++-4.9 + ln -s clang-3.6 gcc-4.9 + ln -s clang-3.6 cpp-4.9 + ln -s clang-3.6 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.6 g++-5 + ln -s clang-3.6 gcc-5 + ln -s clang-3.6 cpp-5 + ln -s clang-3.6 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-r7rlVQ/apt_archive/sbuild-build-depends-core-dummy.deb'. OK 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 0 B/816 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), bison, cmake, debhelper (>= 7.0.50~), flex, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libsqlite3-dev, python-dev, python-imaging, python-numpy, python-pandas, python-support Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), bison, cmake, debhelper (>= 7.0.50~), flex, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libsqlite3-dev, python-dev, python-imaging, python-numpy, python-pandas, python-support dpkg-deb: building package `sbuild-build-depends-rdkit-dummy' in `/«BUILDDIR»/resolver-VYcc8x/apt_archive/sbuild-build-depends-rdkit-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install rdkit build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bison bsdmainutils cmake cmake-data debhelper file flex gettext gettext-base groff-base icu-devtools intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-common libblas3 libboost-atomic1.55-dev libboost-atomic1.55.0 libboost-chrono1.55-dev libboost-chrono1.55.0 libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-dev libboost-python-dev libboost-python1.55-dev libboost-python1.55.0 libboost-regex-dev libboost-regex1.55-dev libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-system-dev libboost-system1.55-dev libboost-system1.55.0 libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0 libboost1.55-dev libcroco3 libcurl3 libexpat1 libexpat1-dev libfl-dev libfreetype6 libgfortran3 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libicu-dev libicu52 libidn11 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 libpng12-0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl1.0.0 libtasn1-6 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1 libxml2 m4 man-db mime-support po-debconf python python-dateutil python-dev python-imaging python-minimal python-numpy python-pandas python-pandas-lib python-pil python-six python-support python-tz python2.7 python2.7-dev python2.7-minimal Suggested packages: bison-doc wamerican wordlist whois vacation codeblocks eclipse ninja-build dh-make gettext-doc groff lrzip libboost-doc libboost1.55-doc gccxml python3 libboost-context1.55-dev libboost-coroutine1.55-dev libboost-exception1.55-dev libboost-filesystem1.55-dev libboost-graph1.55-dev libboost-graph-parallel1.55-dev libboost-iostreams1.55-dev libboost-locale1.55-dev libboost-log1.55-dev libboost-math1.55-dev libboost-mpi1.55-dev libboost-mpi-python1.55-dev libboost-program-options1.55-dev libboost-random1.55-dev libboost-signals1.55-dev libboost-test1.55-dev libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev libmpfrc++-dev libntl-dev gnutls-bin krb5-doc krb5-user icu-doc liblcms2-utils sqlite3-doc www-browser libmail-box-perl python-doc python-tk gfortran python-nose python-numpy-dbg python-numpy-doc python-pandas-doc python-pil-doc python-pil-dbg python2.7-doc binfmt-support Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libsasl2-modules xml-core libmail-sendmail-perl python-scipy python-matplotlib python-tables python-numexpr python-xlrd python-statsmodels python-openpyxl python-xlwt python-bs4 python-html5lib The following NEW packages will be installed: bison bsdmainutils cmake cmake-data debhelper file flex gettext gettext-base groff-base icu-devtools intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-common libblas3 libboost-atomic1.55-dev libboost-atomic1.55.0 libboost-chrono1.55-dev libboost-chrono1.55.0 libboost-date-time1.55-dev libboost-date-time1.55.0 libboost-dev libboost-python-dev libboost-python1.55-dev libboost-python1.55.0 libboost-regex-dev libboost-regex1.55-dev libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-system-dev libboost-system1.55-dev libboost-system1.55.0 libboost-thread-dev libboost-thread1.55-dev libboost-thread1.55.0 libboost1.55-dev libcroco3 libcurl3 libexpat1 libexpat1-dev libfl-dev libfreetype6 libgfortran3 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libicu-dev libicu52 libidn11 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 libpng12-0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl1.0.0 libtasn1-6 libtiff5 libunistring0 libwebp5 libwebpdemux1 libwebpmux1 libxml2 m4 man-db mime-support po-debconf python python-dateutil python-dev python-imaging python-minimal python-numpy python-pandas python-pandas-lib python-pil python-six python-support python-tz python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-rdkit-dummy 0 upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 74.3 MB/74.3 MB of archives. After this operation, 325 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.4.0-1 [27.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1k-3 [1037 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.3-1 [1205 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.6 [183 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.7.0.2-5 [1000 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.3-2 [31.3 kB] Get:7 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-5 [176 kB] Get:8 http://localhost:9999/debian/ unstable/main libhogweed2 amd64 2.7.1-5 [125 kB] Get:9 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.20.7-1 [81.2 kB] Get:10 http://localhost:9999/debian/ unstable/main libtasn1-6 amd64 4.2-2 [48.6 kB] Get:11 http://localhost:9999/debian/ unstable/main libgnutls-deb0-28 amd64 3.3.8-6 [694 kB] Get:12 http://localhost:9999/debian/ unstable/main libkeyutils1 amd64 1.5.9-5+b1 [12.0 kB] Get:13 http://localhost:9999/debian/ unstable/main libkrb5support0 amd64 1.12.1+dfsg-19 [58.5 kB] Get:14 http://localhost:9999/debian/ unstable/main libk5crypto3 amd64 1.12.1+dfsg-19 [115 kB] Get:15 http://localhost:9999/debian/ unstable/main libkrb5-3 amd64 1.12.1+dfsg-19 [303 kB] Get:16 http://localhost:9999/debian/ unstable/main libgssapi-krb5-2 amd64 1.12.1+dfsg-19 [150 kB] Get:17 http://localhost:9999/debian/ unstable/main libidn11 amd64 1.29-1+b2 [136 kB] Get:18 http://localhost:9999/debian/ unstable/main libsasl2-modules-db amd64 2.1.26.dfsg1-13 [67.0 kB] Get:19 http://localhost:9999/debian/ unstable/main libsasl2-2 amd64 2.1.26.dfsg1-13 [104 kB] Get:20 http://localhost:9999/debian/ unstable/main libldap-2.4-2 amd64 2.4.40-4 [217 kB] Get:21 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:22 http://localhost:9999/debian/ unstable/main libsqlite3-0 amd64 3.8.7.4-1 [439 kB] Get:23 http://localhost:9999/debian/ unstable/main libicu52 amd64 52.1-8 [6780 kB] Get:24 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.2+dfsg1-3 [934 kB] Get:25 http://localhost:9999/debian/ unstable/main libpython2.7-minimal amd64 2.7.9-2 [376 kB] Get:26 http://localhost:9999/debian/ unstable/main python2.7-minimal amd64 2.7.9-2 [1401 kB] Get:27 http://localhost:9999/debian/ unstable/main python-minimal amd64 2.7.9-1 [40.3 kB] Get:28 http://localhost:9999/debian/ unstable/main mime-support all 3.58 [36.0 kB] Get:29 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-6+b3 [80.3 kB] Get:30 http://localhost:9999/debian/ unstable/main libpython2.7-stdlib amd64 2.7.9-2 [1844 kB] Get:31 http://localhost:9999/debian/ unstable/main python2.7 amd64 2.7.9-2 [251 kB] Get:32 http://localhost:9999/debian/ unstable/main libpython-stdlib amd64 2.7.9-1 [19.5 kB] Get:33 http://localhost:9999/debian/ unstable/main python amd64 2.7.9-1 [151 kB] Get:34 http://localhost:9999/debian/ unstable/main cmake-data all 3.0.2-1 [929 kB] Get:35 http://localhost:9999/debian/ unstable/main liblzo2-2 amd64 2.08-1.2 [54.6 kB] Get:36 http://localhost:9999/debian/ unstable/main libarchive13 amd64 3.1.2-11 [269 kB] Get:37 http://localhost:9999/debian/ unstable/main librtmp1 amd64 2.4+20131018.git79459a2-5 [59.6 kB] Get:38 http://localhost:9999/debian/ unstable/main libssh2-1 amd64 1.4.3-4.1 [125 kB] Get:39 http://localhost:9999/debian/ unstable/main libcurl3 amd64 7.38.0-4 [259 kB] Get:40 http://localhost:9999/debian/ unstable/main cmake amd64 3.0.2-1 [2384 kB] Get:41 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-4+b1 [29.2 kB] Get:42 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.17-4 [254 kB] Get:43 http://localhost:9999/debian/ unstable/main libfl-dev amd64 2.5.39-8+b1 [75.4 kB] Get:44 http://localhost:9999/debian/ unstable/main flex amd64 2.5.39-8+b1 [422 kB] Get:45 http://localhost:9999/debian/ unstable/main libboost-atomic1.55.0 amd64 1.55.0+dfsg-3 [28.4 kB] Get:46 http://localhost:9999/debian/ unstable/main libboost-system1.55.0 amd64 1.55.0+dfsg-3 [30.2 kB] Get:47 http://localhost:9999/debian/ unstable/main libboost-chrono1.55.0 amd64 1.55.0+dfsg-3 [35.1 kB] Get:48 http://localhost:9999/debian/ unstable/main libboost-date-time1.55.0 amd64 1.55.0+dfsg-3 [41.5 kB] Get:49 http://localhost:9999/debian/ unstable/main libboost-python1.55.0 amd64 1.55.0+dfsg-3 [146 kB] Get:50 http://localhost:9999/debian/ unstable/main libboost-regex1.55.0 amd64 1.55.0+dfsg-3 [293 kB] Get:51 http://localhost:9999/debian/ unstable/main libboost-serialization1.55.0 amd64 1.55.0+dfsg-3 [153 kB] Get:52 http://localhost:9999/debian/ unstable/main libboost-thread1.55.0 amd64 1.55.0+dfsg-3 [53.4 kB] Get:53 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.42.1-1 [2401 kB] Get:54 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:55 http://localhost:9999/debian/ unstable/main libpng12-0 amd64 1.2.50-2+b2 [172 kB] Get:56 http://localhost:9999/debian/ unstable/main libfreetype6 amd64 2.5.2-4 [466 kB] Get:57 http://localhost:9999/debian/ unstable/main libgfortran3 amd64 4.9.2-10 [255 kB] Get:58 http://localhost:9999/debian/ unstable/main liblcms2-2 amd64 2.6-3+b3 [141 kB] Get:59 http://localhost:9999/debian/ unstable/main libpython2.7 amd64 2.7.9-2 [1080 kB] Get:60 http://localhost:9999/debian/ unstable/main libexpat1-dev amd64 2.1.0-6+b3 [126 kB] Get:61 http://localhost:9999/debian/ unstable/main libpython2.7-dev amd64 2.7.9-2 [18.6 MB] Get:62 http://localhost:9999/debian/ unstable/main libjbig0 amd64 2.1-3.1 [30.7 kB] Get:63 http://localhost:9999/debian/ unstable/main libjpeg62-turbo amd64 1:1.3.1-12 [116 kB] Get:64 http://localhost:9999/debian/ unstable/main libtiff5 amd64 4.0.3-12.3 [217 kB] Get:65 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:66 http://localhost:9999/debian/ unstable/main libwebp5 amd64 0.4.1-1.2+b2 [201 kB] Get:67 http://localhost:9999/debian/ unstable/main libwebpdemux1 amd64 0.4.1-1.2+b2 [50.7 kB] Get:68 http://localhost:9999/debian/ unstable/main libwebpmux1 amd64 0.4.1-1.2+b2 [57.2 kB] Get:69 http://localhost:9999/debian/ unstable/main file amd64 1:5.22+15-2 [60.1 kB] Get:70 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.3-2 [121 kB] Get:71 http://localhost:9999/debian/ unstable/main python-support all 1.0.15 [33.6 kB] Get:72 http://localhost:9999/debian/ unstable/main libbison-dev amd64 2:3.0.2.dfsg-2 [426 kB] Get:73 http://localhost:9999/debian/ unstable/main bison amd64 2:3.0.2.dfsg-2 [765 kB] Get:74 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.3-2 [1240 kB] Get:75 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:76 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:77 http://localhost:9999/debian/ unstable/main debhelper all 9.20150101 [813 kB] Get:78 http://localhost:9999/debian/ unstable/main icu-devtools amd64 52.1-8 [172 kB] Get:79 http://localhost:9999/debian/ unstable/main libblas-common amd64 1.2.20110419-10 [8496 B] Get:80 http://localhost:9999/debian/ unstable/main libblas3 amd64 1.2.20110419-10 [167 kB] Get:81 http://localhost:9999/debian/ unstable/main libboost1.55-dev amd64 1.55.0+dfsg-3 [5818 kB] Get:82 http://localhost:9999/debian/ unstable/main libboost-atomic1.55-dev amd64 1.55.0+dfsg-3 [27.2 kB] Get:83 http://localhost:9999/debian/ unstable/main libboost-chrono1.55-dev amd64 1.55.0+dfsg-3 [36.9 kB] Get:84 http://localhost:9999/debian/ unstable/main libboost-serialization1.55-dev amd64 1.55.0+dfsg-3 [191 kB] Get:85 http://localhost:9999/debian/ unstable/main libboost-date-time1.55-dev amd64 1.55.0+dfsg-3 [48.9 kB] Get:86 http://localhost:9999/debian/ unstable/main libboost-dev amd64 1.55.0.2 [3368 B] Get:87 http://localhost:9999/debian/ unstable/main libpython-dev amd64 2.7.9-1 [19.6 kB] Get:88 http://localhost:9999/debian/ unstable/main python2.7-dev amd64 2.7.9-2 [276 kB] Get:89 http://localhost:9999/debian/ unstable/main python-dev amd64 2.7.9-1 [1182 B] Get:90 http://localhost:9999/debian/ unstable/main libboost-python1.55-dev amd64 1.55.0+dfsg-3 [174 kB] Get:91 http://localhost:9999/debian/ unstable/main libboost-python-dev amd64 1.55.0.2 [3410 B] Get:92 http://localhost:9999/debian/ unstable/main libicu-dev amd64 52.1-8 [7645 kB] Get:93 http://localhost:9999/debian/ unstable/main libboost-regex1.55-dev amd64 1.55.0+dfsg-3 [352 kB] Get:94 http://localhost:9999/debian/ unstable/main libboost-regex-dev amd64 1.55.0.2 [3276 B] Get:95 http://localhost:9999/debian/ unstable/main libboost-system1.55-dev amd64 1.55.0+dfsg-3 [30.6 kB] Get:96 http://localhost:9999/debian/ unstable/main libboost-system-dev amd64 1.55.0.2 [3152 B] Get:97 http://localhost:9999/debian/ unstable/main libboost-thread1.55-dev amd64 1.55.0+dfsg-3 [54.0 kB] Get:98 http://localhost:9999/debian/ unstable/main libboost-thread-dev amd64 1.55.0.2 [3034 B] Get:99 http://localhost:9999/debian/ unstable/main liblapack3 amd64 3.5.0-4 [1852 kB] Get:100 http://localhost:9999/debian/ unstable/main libsqlite3-dev amd64 3.8.7.4-1 [538 kB] Get:101 http://localhost:9999/debian/ unstable/main python-six all 1.8.0-1 [12.6 kB] Get:102 http://localhost:9999/debian/ unstable/main python-dateutil all 2.2-2 [51.3 kB] Get:103 http://localhost:9999/debian/ unstable/main python-pil amd64 2.6.1-2 [304 kB] Get:104 http://localhost:9999/debian/ unstable/main python-imaging all 2.6.1-2 [9614 B] Get:105 http://localhost:9999/debian/ unstable/main python-numpy amd64 1:1.8.2-2 [1630 kB] Get:106 http://localhost:9999/debian/ unstable/main python-tz all 2012c+dfsg-0.1 [31.9 kB] Get:107 http://localhost:9999/debian/ unstable/main python-pandas-lib amd64 0.15.1+git125-ge463818-1 [1456 kB] Get:108 http://localhost:9999/debian/ unstable/main python-pandas all 0.15.1+git125-ge463818-1 [1384 kB] Extracting templates from packages: 27% Extracting templates from packages: 55% Extracting templates from packages: 82% Extracting templates from packages: 100% Preconfiguring packages ... 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Processing triggers for libc-bin (2.19-17) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-17 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt7-1 Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.7 apt-utils_1.0.9.7 base-files_8 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-5 bison_2:3.0.2.dfsg-2 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7+b2 clang-3.6_1:3.6-2 cmake_3.0.2-1 cmake-data_3.0.2-1 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9+b1 flex_2.5.39-8+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 icu-devtools_52.1-8 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 less_458-3 libacl1_2.2.52-2 libapt-inst1.5_1.0.9.7 libapt-pkg4.12_1.0.9.7 libarchive13_3.1.2-11 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libbison-dev_2:3.0.2.dfsg-2 libblas-common_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.25.2-5 libboost-atomic1.55-dev_1.55.0+dfsg-3 libboost-atomic1.55.0_1.55.0+dfsg-3 libboost-chrono1.55-dev_1.55.0+dfsg-3 libboost-chrono1.55.0_1.55.0+dfsg-3 libboost-date-time1.55-dev_1.55.0+dfsg-3 libboost-date-time1.55.0_1.55.0+dfsg-3 libboost-dev_1.55.0.2 libboost-python-dev_1.55.0.2 libboost-python1.55-dev_1.55.0+dfsg-3 libboost-python1.55.0_1.55.0+dfsg-3 libboost-regex-dev_1.55.0.2 libboost-regex1.55-dev_1.55.0+dfsg-3 libboost-regex1.55.0_1.55.0+dfsg-3 libboost-serialization1.55-dev_1.55.0+dfsg-3 libboost-serialization1.55.0_1.55.0+dfsg-3 libboost-system-dev_1.55.0.2 libboost-system1.55-dev_1.55.0+dfsg-3 libboost-system1.55.0_1.55.0+dfsg-3 libboost-thread-dev_1.55.0.2 libboost-thread1.55-dev_1.55.0+dfsg-3 libboost-thread1.55.0_1.55.0+dfsg-3 libboost1.55-dev_1.55.0+dfsg-3 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7+b2 libc-bin_2.19-17 libc-dev-bin_2.19-17 libc6_2.19-17 libc6-dev_2.19-17 libcap2_1:2.24-7 libcap2-bin_1:2.24-7 libcilkrts5_4.9.2-10 libclang-common-3.6-dev_1:3.6-2 libclang1-3.6_1:3.6-2 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libcurl3_7.38.0-4 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.1 libdpkg-perl_1.17.24 libedit2_3.1-20140620-2 libexpat1_2.1.0-6+b3 libexpat1-dev_2.1.0-6+b3 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libfl-dev_2.5.39-8+b1 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran3_4.9.2-10 libglib2.0-0_2.42.1-1 libgmp10_2:6.0.0+dfsg-6 libgnutls-deb0-28_3.3.8-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libgssapi-krb5-2_1.12.1+dfsg-19 libhogweed2_2.7.1-5 libicu-dev_52.1-8 libicu52_52.1-8 libidn11_1.29-1+b2 libisl10_0.12.2-2 libitm1_4.9.2-10 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.3.1-12 libk5crypto3_1.12.1+dfsg-19 libkeyutils1_1.5.9-5+b1 libkmod2_20-1 libkrb5-3_1.12.1+dfsg-19 libkrb5support0_1.12.1+dfsg-19 liblapack3_3.5.0-4 liblcms2-2_2.6-3+b3 libldap-2.4-2_2.4.40-4 libllvm3.6_1:3.6-2 liblsan0_4.9.2-10 liblzma5_5.1.1alpha+20120614-2+b3 liblzo2-2_2.08-1.2 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.3-1 libmpfr4_3.1.2-3 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libnettle4_2.7.1-5 libobjc-4.9-dev_4.9.2-10 libobjc4_4.9.2-10 libp11-kit0_0.20.7-1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.9-2 libpython2.7-dev_2.7.9-2 libpython2.7-minimal_2.7.9-2 libpython2.7-stdlib_2.7.9-2 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 librtmp1_2.4+20131018.git79459a2-5 libsasl2-2_2.1.26.dfsg1-13 libsasl2-modules-db_2.1.26.dfsg1-13 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libsigsegv2_2.10-4+b1 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libsqlite3-0_3.8.7.4-1 libsqlite3-dev_3.8.7.4-1 libss2_1.42.12-1.1 libssh2-1_1.4.3-4.1 libssl1.0.0_1.0.1k-3 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libtasn1-6_4.2-2 libtiff5_4.0.3-12.3 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-12 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-5 libwebp5_0.4.1-1.2+b2 libwebpdemux1_0.4.1-1.2+b2 libwebpmux1_0.4.1-1.2+b2 libxml2_2.9.2+dfsg1-3 linux-libc-dev_3.16.7-ckt7-1 login_1:4.2-3 lsb-base_4.1+Debian13+nmu1 m4_1.4.17-4 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.25.2-5 multiarch-support_2.19-17 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 nvi_1.81.6-11+b1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-2 perl-base_5.20.2-2 perl-modules_5.20.2-2 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 python_2.7.9-1 python-dateutil_2.2-2 python-dev_2.7.9-1 python-imaging_2.6.1-2 python-minimal_2.7.9-1 python-numpy_1:1.8.2-2 python-pandas_0.15.1+git125-ge463818-1 python-pandas-lib_0.15.1+git125-ge463818-1 python-pil_2.6.1-2 python-six_1.8.0-1 python-support_1.0.15 python-tz_2012c+dfsg-0.1 python2.7_2.7.9-2 python2.7-dev_2.7.9-2 python2.7-minimal_2.7.9-2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rdkit-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.12-1 systemd_215-12 systemd-sysv_215-12 sysv-rc_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2+b1 tzdata_2015b-1 udev_215-12 util-linux_2.25.2-5 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Oct 25 17:50:24 2014 UTC using RSA key ID B43481B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./rdkit_201403-1.dsc dpkg-source: info: extracting rdkit in rdkit-201403 dpkg-source: info: unpacking rdkit_201403.orig.tar.gz dpkg-source: info: unpacking rdkit_201403-1.debian.tar.xz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-94cbf51d-9f77-48e3-93d9-1ea603e96b2f SCHROOT_UID=1001 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package rdkit dpkg-buildpackage: source version 201403-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Michael Banck dpkg-source --before-build rdkit-201403 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --buildsystem=cmake --parallel dh_testdir -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/«PKGBUILDDIR»' find /«PKGBUILDDIR» -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ Code/RDGeneral/versions.h rdkit/Chem/inchi.py dh_auto_clean make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean -O--buildsystem=cmake -O--parallel debian/rules build-arch dh build-arch --with python2 --buildsystem=cmake --parallel dh_testdir -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/«PKGBUILDDIR»' 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 -- The C compiler identification is Clang 3.6.0 -- The CXX compiler identification is Clang 3.6.0 -- 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 -- 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 -- 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 PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.9") -- Found PythonInterp: /usr/bin/python (found version "2.7.9") -- Boost version: 1.55.0 -- Found the following Boost libraries: -- python Python Install directory /usr/lib/python2.7/dist-packages -- Looking for include file pthread.h -- Looking for include file 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: 1.55.0 -- Found the following Boost libraries: -- thread -- system -- Boost version: 1.55.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /«PKGBUILDDIR»/obj-x86_64-linux-gnu make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_build -a -O--buildsystem=cmake -O--parallel make[1]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -H/«PKGBUILDDIR» -B/«PKGBUILDDIR»/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' 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/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/External/INCHI-API /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/External/INCHI-API /«PKGBUILDDIR»/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ML/InfoTheory /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/RDBoost /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ChemicalFeatures /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/RDGeneral /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= Scanning dependencies of target inchi_support Scanning dependencies of target hc Scanning dependencies of target InfoTheory make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build Scanning dependencies of target ChemicalFeatures Scanning dependencies of target RDBoost make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /«PKGBUILDDIR»/External/INCHI-API/python/noinchi.py /«PKGBUILDDIR»/rdkit/Chem/inchi.py make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build Scanning dependencies of target RDGeneral make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 66 make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 48 make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 49 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 0%] [ 0%] [ 1%] [ 1%] make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 2%] [ 2%] [ 2%] [ 3%] [ 3%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o [ 3%] cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /«PKGBUILDDIR»/Code/ML/InfoTheory/InfoBitRanker.cpp Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -Dhc_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/hc.dir/hcdriver.c.o -c /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh/hcdriver.c Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o Built target inchi_support Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DChemicalFeatures_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /«PKGBUILDDIR»/Code/ChemicalFeatures/FreeChemicalFeature.cpp Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DRDBoost_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /«PKGBUILDDIR»/Code/RDBoost/Wrap.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -Dhc_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/hc.dir/hc.c.o -c /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh/hc.c Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/Invariant.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/utils.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/types.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/RDLog.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeneral.dir/Dict.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/Dict.cpp Linking C shared library ../../../../lib/libhc.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libhc.so.1 -o ../../../../lib/libhc.so.1.2014.03.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libhc.so.1.2014.03.1 ../../../../lib/libhc.so.1 ../../../../lib/libhc.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 66 [ 3%] Built target hc Linking CXX static library libInfoTheory.a cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -P CMakeFiles/InfoTheory.dir/cmake_clean_target.cmake cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/ar cr libInfoTheory.a CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o /usr/bin/ranlib libInfoTheory.a make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 3%] Built target InfoTheory Linking CXX shared library ../../lib/libRDGeneral.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libRDGeneral.so.1 -o ../../lib/libRDGeneral.so.1.2014.03.1 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/Dict.cpp.o Linking CXX shared library ../../lib/libChemicalFeatures.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libChemicalFeatures.so.1 -o ../../lib/libChemicalFeatures.so.1.2014.03.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libChemicalFeatures.so.1.2014.03.1 ../../lib/libChemicalFeatures.so.1 ../../lib/libChemicalFeatures.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDGeneral.so.1.2014.03.1 ../../lib/libRDGeneral.so.1 ../../lib/libRDGeneral.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 49 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 3%] Built target ChemicalFeatures [ 3%] Built target RDGeneral make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/DataManip/MetricMatrixCalc /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/RDGeneral /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ChemicalFeatures /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/Query /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Query /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/Numerics/EigenSolvers /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/Numerics /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/Catalogs /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/SimDivPickers /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/DataStructs /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target testQuery Scanning dependencies of target testMatCalc Scanning dependencies of target EigenSolvers Scanning dependencies of target testDict make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build Scanning dependencies of target testChemicalFeatures Scanning dependencies of target testMatrices Linking CXX shared library ../../lib/libRDBoost.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build Scanning dependencies of target Catalogs make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build Scanning dependencies of target SimDivPickers make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 93 Scanning dependencies of target DataStructs make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 14 make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 54 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 3%] [ 3%] [ 3%] [ 4%] [ 4%] /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libRDBoost.so.1 -o ../../lib/libRDBoost.so.1.2014.03.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread [ 4%] [ 5%] [ 6%] [ 6%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /«PKGBUILDDIR»/Code/ChemicalFeatures/testChemicalFeatures.cpp Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /«PKGBUILDDIR»/Code/Numerics/testMatrices.cpp Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testDict.dir/testDict.cpp.o -c /«PKGBUILDDIR»/Code/RDGeneral/testDict.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /«PKGBUILDDIR»/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testQuery.dir/test.cpp.o -c /«PKGBUILDDIR»/Code/Query/test.cpp Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /«PKGBUILDDIR»/Code/Catalogs/Catalog.cpp Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DEigenSolvers_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /«PKGBUILDDIR»/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/DistPicker.cpp Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/BitVect.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDBoost.so.1.2014.03.1 ../../lib/libRDBoost.so.1 ../../lib/libRDBoost.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 48 [ 6%] Built target RDBoost /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 1 [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /«PKGBUILDDIR»/Code/Catalogs/CatalogParams.cpp make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/RDBoost/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= Scanning dependencies of target rdBase make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 7%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdBase_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /«PKGBUILDDIR»/Code/RDBoost/Wrap/RDBase.cpp Linking CXX executable testMatCalc cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc -rdynamic ../../../lib/libRDGeneral.so.1.2014.03.1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 93 [ 7%] Built target testMatCalc make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Scanning dependencies of target Clustering make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 5 [ 8%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DClustering_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh/Clustering.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/MaxMinPicker.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/SparseBitVect.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /«PKGBUILDDIR»/Code/Catalogs/CatalogEntry.cpp Linking CXX shared library ../../lib/libCatalogs.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libCatalogs.so.1 -o ../../lib/libCatalogs.so.1.2014.03.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDGeneral.so.1.2014.03.1 cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libCatalogs.so.1.2014.03.1 ../../lib/libCatalogs.so.1 ../../lib/libCatalogs.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 1 [ 8%] Built target Catalogs /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/HierarchicalClusterPicker.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 6 [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/ExplicitBitVect.cpp Linking CXX executable testChemicalFeatures cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures -rdynamic ../../lib/libChemicalFeatures.so.1.2014.03.1 ../../lib/libRDGeneral.so.1.2014.03.1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 9%] Built target testChemicalFeatures make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ML/Data /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Data /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Linking CXX shared library ../../../lib/libEigenSolvers.so Scanning dependencies of target cQuantize cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 62 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libEigenSolvers.so.1 -o ../../../lib/libEigenSolvers.so.1.2014.03.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDGeneral.so.1.2014.03.1 [ 10%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcQuantize_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /«PKGBUILDDIR»/Code/ML/Data/cQuantize.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libEigenSolvers.so.1.2014.03.1 ../../../lib/libEigenSolvers.so.1 ../../../lib/libEigenSolvers.so Linking CXX executable testQuery cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 14 [ 10%] /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testQuery.dir/test.cpp.o -o testQuery -rdynamic ../../lib/libRDGeneral.so.1.2014.03.1 Built target EigenSolvers /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Utils.cpp make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 10%] Built target testQuery /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/base64.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 7 [ 11%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/BitOps.cpp In file included from /«PKGBUILDDIR»/Code/ML/Cluster/Murtagh/Clustering.cpp:17: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 11%] /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o Linking CXX executable testMatrices cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/DiscreteDistMat.cpp [ 11%] /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices -rdynamic ../../lib/libRDGeneral.so.1.2014.03.1 Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/DiscreteValueVect.cpp make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 11%] Built target testMatrices Linking CXX shared library ../../lib/libSimDivPickers.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libSimDivPickers.so.1 -o ../../lib/libSimDivPickers.so.1.2014.03.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libhc.so.1.2014.03.1 ../../lib/libRDGeneral.so.1.2014.03.1 cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libSimDivPickers.so.1.2014.03.1 ../../lib/libSimDivPickers.so.1 ../../lib/libSimDivPickers.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 54 [ 11%] Built target SimDivPickers 1 warning generated. Linking CXX executable testDict cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testDict.dir/testDict.cpp.o -o testDict -rdynamic ../../lib/libRDGeneral.so.1.2014.03.1 Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,Clustering.so -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libhc.so.1.2014.03.1 ../../../../lib/libRDGeneral.so.1.2014.03.1 ../../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 11%] Built target testDict make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 5 [ 11%] Built target Clustering Linking CXX shared library ../../lib/libDataStructs.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libDataStructs.so.1 -o ../../lib/libDataStructs.so.1.2014.03.1 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o ../../lib/libRDGeneral.so.1.2014.03.1 cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libDataStructs.so.1.2014.03.1 ../../lib/libDataStructs.so.1 ../../lib/libDataStructs.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 6 7 [ 11%] Built target DataStructs make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/DataManip/MetricMatrixCalc/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/Geometry /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/DataStructs /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/SimDivPickers/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/Code/DataStructs/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target RDGeometryLib Scanning dependencies of target rdMetricMatrixCalc Scanning dependencies of target testDataStructs make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' Scanning dependencies of target rdInfoTheory make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build Scanning dependencies of target rdSimDivPickers make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' Scanning dependencies of target cDataStructs /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 50 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 71 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 76 make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 11%] [ 11%] [ 12%] [ 12%] [ 13%] [ 14%] [ 14%] [ 14%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/testDatastructs.cpp Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdMetricMatrixCalc_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /«PKGBUILDDIR»/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /«PKGBUILDDIR»/Code/Geometry/point.cpp Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdInfoTheory_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /«PKGBUILDDIR»/Code/Geometry/Transform2D.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/MaxMinPicker.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdInfoTheory_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/DataStructs.cpp In file included from /«PKGBUILDDIR»/Code/ML/Data/cQuantize.cpp:15: In file included from /usr/include/python2.7/numpy/oldnumeric.h:1: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ 1 warning generated. Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,cQuantize.so -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../InfoTheory/libInfoTheory.a ../../../lib/libRDGeneral.so.1.2014.03.1 ../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 62 [ 14%] Built target cQuantize /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdInfoTheory_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp In file included from /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:14: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:15: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /«PKGBUILDDIR»/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:14: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:16: In file included from /usr/include/python2.7/numpy/oldnumeric.h:1: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/DiscreteValueVect.cpp In file included from /«PKGBUILDDIR»/Code/DataStructs/Wrap/DataStructs.cpp:20: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /«PKGBUILDDIR»/Code/Geometry/Transform3D.cpp 1 warning generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp 1 warning generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 51 [ 15%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /«PKGBUILDDIR»/Code/Geometry/UniformGrid3D.cpp 1 warning generated. Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,rdMetricMatrixCalc.so -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDGeneral.so.1.2014.03.1 ../../../../lib/libDataStructs.so.1.2014.03.1 ../../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread ../../../../lib/libRDGeneral.so.1.2014.03.1 In file included from /«PKGBUILDDIR»/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:12: In file included from /usr/include/python2.7/numpy/oldnumeric.h:1: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 15%] Built target rdMetricMatrixCalc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 60 [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/SparseIntVect.cpp 1 warning generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 16%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /«PKGBUILDDIR»/Code/Geometry/GridUtils.cpp 1 warning generated. Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,rdInfoTheory.so -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../libInfoTheory.a ../../../../lib/libRDGeneral.so.1.2014.03.1 ../../../../lib/libDataStructs.so.1.2014.03.1 ../../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread ../../../../lib/libRDGeneral.so.1.2014.03.1 /usr/bin/ld: ../libInfoTheory.a(InfoBitRanker.cpp.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC ../libInfoTheory.a: error adding symbols: Bad value clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: *** [rdkit/ML/InfoTheory/rdInfoTheory.so] Error 1 Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make:148: recipe for target 'rdkit/ML/InfoTheory/rdInfoTheory.so' failed make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[2]: *** [Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all] Error 2 CMakeFiles/Makefile2:5664: recipe for target 'Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/all' failed make[2]: *** Waiting for unfinished jobs.... /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/wrap_SparseBV.cpp Linking CXX executable testDataStructs cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs -rdynamic ../../lib/libDataStructs.so.1.2014.03.1 ../../lib/libRDGeneral.so.1.2014.03.1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 16%] Built target testDataStructs /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 61 [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp 1 warning generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 17%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DrdSimDivPickers_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/wrap_BitOps.cpp In file included from /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:16: In file included from /usr/include/python2.7/numpy/oldnumeric.h:1: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DRDK_64BIT_BUILD -DRDK_THREADSAFE_SSS -DcDataStructs_EXPORTS -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -I/«PKGBUILDDIR»/Code -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /«PKGBUILDDIR»/Code/DataStructs/Wrap/wrap_Utils.cpp 1 warning generated. Linking CXX shared library ../../lib/libRDGeometryLib.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,libRDGeometryLib.so.1 -o ../../lib/libRDGeometryLib.so.1.2014.03.1 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libDataStructs.so.1.2014.03.1 ../../lib/libRDGeneral.so.1.2014.03.1 cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDGeometryLib.so.1.2014.03.1 ../../lib/libRDGeometryLib.so.1 ../../lib/libRDGeometryLib.so make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 50 51 [ 17%] Built target RDGeometryLib In file included from /«PKGBUILDDIR»/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:13: In file included from /usr/include/python2.7/numpy/oldnumeric.h:1: In file included from /usr/include/python2.7/numpy/arrayobject.h:4: In file included from /usr/include/python2.7/numpy/ndarrayobject.h:17: In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ 1 warning generated. Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,rdSimDivPickers.so -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libSimDivPickers.so.1.2014.03.1 ../../../lib/libhc.so.1.2014.03.1 ../../../lib/libDataStructs.so.1.2014.03.1 ../../../lib/libRDGeneral.so.1.2014.03.1 ../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 76 [ 17%] Built target rdSimDivPickers Linking CXX shared module ../../../rdkit/rdBase.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,rdBase.so -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDGeneral.so.1.2014.03.1 ../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 17%] Built target rdBase Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -shared -Wl,-soname,cDataStructs.so -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_Utils.cpp.o ../../../lib/libRDGeneral.so.1.2014.03.1 ../../../lib/libDataStructs.so.1.2014.03.1 ../../../lib/libRDBoost.so.1.2014.03.1 -lpython2.7 -lboost_python -lboost_thread -lboost_system -lpthread ../../../lib/libRDGeneral.so.1.2014.03.1 make[3]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 60 61 [ 17%] Built target cDataStructs make[2]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[1]: *** [all] Error 2 Makefile:150: recipe for target 'all' failed make[1]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' dh_auto_build: make -j10 returned exit code 2 make: *** [build-arch] Error 2 debian/rules:18: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150326-1041 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 185820 Build-Time: 112 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 35 Job: rdkit_201403-1 Machine Architecture: amd64 Package: rdkit Package-Time: 185 Source-Version: 201403-1 Space: 185820 Status: attempted Version: 201403-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150326-1041 Build needed 00:03:05, 185820k disc space DC-Status: Failed 186.531964277s DC-Time-Estimation: 186.531964277 versus expected 5168 (r/m: 26.705707276665567 ; m: 186.531964277)