DC-Build-Header: python-cogent 1.5.1-2 / Sat Jun 23 16:32:56 +0000 2012 DC-Task: logfile:/tmp/python-cogent_1.5.1-2_unstable_clang.log version:1.5.1-2 chroot:unstable modes:binary-only:clang source:python-cogent architecture:any esttime:103 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang python-cogent_1.5.1-2' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-201-111.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ python-cogent 1.5.1-2 (amd64) 23 Jun 2012 16:32 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: python-cogent Version: 1.5.1-2 Source Version: 1.5.1-2 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-cogent-vJU6Zc/python-cogent-1.5.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/python-cogent-vJU6Zc' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-92ea38c6-5768-42f1-aaac-d75bcacfa32b' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [233 kB] Get:3 http://localhost unstable/main Sources/DiffIndex [7876 B] Get:4 http://localhost unstable/main amd64 Packages/DiffIndex [7876 B] Get:5 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:6 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:7 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:8 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:9 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:10 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:11 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:12 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:13 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:14 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:15 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Get:16 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:17 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Fetched 296 kB in 7s (41.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-passwd bsdutils libblkid1 libmount1 libuuid1 mount util-linux 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1300 kB of archives. After this operation, 308 kB disk space will be freed. Get:1 http://localhost/debian/ unstable/main mount amd64 2.20.1-5.1 [213 kB] Get:2 http://localhost/debian/ unstable/main util-linux amd64 2.20.1-5.1 [659 kB] Get:3 http://localhost/debian/ unstable/main base-passwd amd64 3.5.26 [46.3 kB] Get:4 http://localhost/debian/ unstable/main bsdutils amd64 1:2.20.1-5.1 [85.3 kB] Get:5 http://localhost/debian/ unstable/main libuuid1 amd64 2.20.1-5.1 [56.9 kB] Get:6 http://localhost/debian/ unstable/main libblkid1 amd64 2.20.1-5.1 [120 kB] Get:7 http://localhost/debian/ unstable/main libmount1 amd64 2.20.1-5.1 [120 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1300 kB in 0s (22.0 MB/s) (Reading database ... 11730 files and directories currently installed.) Preparing to replace mount 2.20.1-5 (using .../mount_2.20.1-5.1_amd64.deb) ... Unpacking replacement mount ... Setting up mount (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace util-linux 2.20.1-5 (using .../util-linux_2.20.1-5.1_amd64.deb) ... Unpacking replacement util-linux ... Setting up util-linux (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace base-passwd 3.5.25 (using .../base-passwd_3.5.26_amd64.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.26) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace bsdutils 1:2.20.1-5 (using .../bsdutils_1%3a2.20.1-5.1_amd64.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libuuid1:amd64 2.20.1-5 (using .../libuuid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libuuid1:amd64 ... Setting up libuuid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libblkid1:amd64 2.20.1-5 (using .../libblkid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libblkid1:amd64 ... Setting up libblkid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libmount1 2.20.1-5 (using .../libmount1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libmount1 ... Setting up libmount1 (2.20.1-5.1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'python-cogent' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/python-cogent/trunk/ Need to get 3065 kB of source archives. Get:1 http://localhost/debian/ unstable/main python-cogent 1.5.1-2 (dsc) [1470 B] Get:2 http://localhost/debian/ unstable/main python-cogent 1.5.1-2 (tar) [3058 kB] Get:3 http://localhost/debian/ unstable/main python-cogent 1.5.1-2 (diff) [5273 B] Fetched 3065 kB in 0s (5734 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-1 [7276 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-6 [84.0 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-6 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (30.0 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11730 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-1_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-6_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-6_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-1) ... Setting up libclang-common-dev (3.1-6) ... Setting up clang (3.1-6) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-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-nGjkPE/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 debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/708 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 ... 11810 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0), python-sphinx, cython Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0), python-sphinx, cython dpkg-deb: building package `sbuild-build-depends-python-cogent-dummy' in `/«BUILDDIR»/resolver-7NLGEM/apt_archive/sbuild-build-depends-python-cogent-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install python-cogent build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cython debhelper docutils-common file gettext gettext-base groff-base html2text intltool-debian libasprintf0c2 libblas3 libblas3gf libcroco3 libdb4.8 libexpat1 libexpat1-dev libgettextpo0 libgfortran3 libglib2.0-0 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblapack3gf libmagic1 libncursesw5 libpcre3 libpipeline1 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-docutils python-jinja2 python-markupsafe python-minimal python-numpy python-pygments python-roman python-sphinx python-support python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev python2.7-minimal sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python-doc python-tk texlive-latex-recommended texlive-latex-base texlive-lang-french fonts-linuxlibertine ttf-linux-libertine python-jinja2-doc python-numpy-doc python-numpy-dbg python-nose gfortran ttf-bitstream-vera jsmath libjs-mathjax texlive-latex-extra texlive-fonts-recommended python2.6-doc binfmt-support python2.7-doc sgml-base-doc Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info javascript-common libgpm2 libssl-doc libmail-sendmail-perl python-imaging libpaper-utils python-lxml docutils-doc python-pkg-resources python-chardet sphinx-doc The following NEW packages will be installed: bsdmainutils cython debhelper docutils-common file gettext gettext-base groff-base html2text intltool-debian libasprintf0c2 libblas3 libblas3gf libcroco3 libdb4.8 libexpat1 libexpat1-dev libgettextpo0 libgfortran3 libglib2.0-0 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblapack3gf libmagic1 libncursesw5 libpcre3 libpipeline1 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-docutils python-jinja2 python-markupsafe python-minimal python-numpy python-pygments python-roman python-sphinx python-support python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-python-cogent-dummy sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 65.4 MB/65.4 MB of archives. After this operation, 161 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libncursesw5 amd64 5.9-9 [141 kB] Get:2 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:3 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-3 [1211 kB] Get:4 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:5 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-1 [250 kB] Get:6 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:7 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.13-1 [455 kB] Get:8 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:9 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:10 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:11 http://localhost/debian/ unstable/main libexpat1 amd64 2.1.0-1 [141 kB] Get:12 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:13 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:14 http://localhost/debian/ unstable/main libgfortran3 amd64 4.7.1-1 [352 kB] Get:15 http://localhost/debian/ unstable/main libdb4.8 amd64 4.8.30-11 [694 kB] Get:16 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:17 http://localhost/debian/ unstable/main groff-base amd64 1.21-8 [1152 kB] Get:18 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:19 http://localhost/debian/ unstable/main file amd64 5.11-1 [53.2 kB] Get:20 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:21 http://localhost/debian/ unstable/main mime-support all 3.52-1 [35.5 kB] Get:22 http://localhost/debian/ unstable/main python2.7-minimal amd64 2.7.3-1 [1770 kB] Get:23 http://localhost/debian/ unstable/main python2.7 amd64 2.7.3-1 [2726 kB] Get:24 http://localhost/debian/ unstable/main python-minimal all 2.7.3~rc2-1 [40.4 kB] Get:25 http://localhost/debian/ unstable/main python all 2.7.3~rc2-1 [179 kB] Get:26 http://localhost/debian/ unstable/main python-support all 1.0.14 [33.5 kB] Get:27 http://localhost/debian/ unstable/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:28 http://localhost/debian/ unstable/main python2.6 amd64 2.6.7-4 [2483 kB] Get:29 http://localhost/debian/ unstable/main cython amd64 0.15.1-2 [1923 kB] Get:30 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:31 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:32 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:33 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:34 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:35 http://localhost/debian/ unstable/main sgml-base all 1.26+nmu3 [13.5 kB] Get:36 http://localhost/debian/ unstable/main xml-core all 0.13+nmu1 [23.8 kB] Get:37 http://localhost/debian/ unstable/main docutils-common all 0.8.1-7 [196 kB] Get:38 http://localhost/debian/ unstable/main libblas3 amd64 1.2.20110419-3 [293 kB] Get:39 http://localhost/debian/ unstable/main libblas3gf amd64 1.2.20110419-3 [7804 B] Get:40 http://localhost/debian/ unstable/main libexpat1-dev amd64 2.1.0-1 [229 kB] Get:41 http://localhost/debian/ unstable/main libjs-jquery all 1.7.2+debian-2 [113 kB] Get:42 http://localhost/debian/ unstable/main libjs-underscore all 1.3.3-1 [42.6 kB] Get:43 http://localhost/debian/ unstable/main libjs-sphinxdoc all 1.1.3+dfsg-4 [43.8 kB] Get:44 http://localhost/debian/ unstable/main liblapack3 amd64 3.4.1-3 [5035 kB] Get:45 http://localhost/debian/ unstable/main liblapack3gf amd64 3.4.1-3 [10.5 kB] Get:46 http://localhost/debian/ unstable/main libpython2.6 amd64 2.6.7-4 [1087 kB] Get:47 http://localhost/debian/ unstable/main libpython2.7 amd64 2.7.3-1 [1212 kB] Get:48 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] Get:49 http://localhost/debian/ unstable/main libssl-dev amd64 1.0.1c-3 [1696 kB] Get:50 http://localhost/debian/ unstable/main python-all all 2.7.3~rc2-1 [880 B] Get:51 http://localhost/debian/ unstable/main python2.7-dev amd64 2.7.3-1 [22.3 MB] Get:52 http://localhost/debian/ unstable/main python-dev all 2.7.3~rc2-1 [912 B] Get:53 http://localhost/debian/ unstable/main python2.6-dev amd64 2.6.7-4 [4832 kB] Get:54 http://localhost/debian/ unstable/main python-all-dev all 2.7.3~rc2-1 [894 B] Get:55 http://localhost/debian/ unstable/main python-roman all 0.8.1-7 [51.9 kB] Get:56 http://localhost/debian/ unstable/main python-docutils all 0.8.1-7 [392 kB] Get:57 http://localhost/debian/ unstable/main python-markupsafe amd64 0.15-1 [14.6 kB] Get:58 http://localhost/debian/ unstable/main python-jinja2 amd64 2.6-1 [168 kB] Get:59 http://localhost/debian/ unstable/main python-numpy amd64 1:1.6.2-1 [2631 kB] Get:60 http://localhost/debian/ unstable/main python-pygments all 1.5+dfsg-1 [451 kB] Get:61 http://localhost/debian/ unstable/main sphinx-common all 1.1.3+dfsg-4 [412 kB] Get:62 http://localhost/debian/ unstable/main python-sphinx all 1.1.3+dfsg-4 [311 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 65.4 MB in 2s (25.6 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 11810 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-9_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.13-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.7.1-1_amd64.deb) ... Selecting previously unselected package libdb4.8:amd64. Unpacking libdb4.8:amd64 (from .../libdb4.8_4.8.30-11_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-8_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.2-1_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-1_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-1_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3~rc2-1_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3~rc2-1_all.deb) ... Selecting previously unselected package python-support. Unpacking python-support (from .../python-support_1.0.14_all.deb) ... Selecting previously unselected package python2.6-minimal. Unpacking python2.6-minimal (from .../python2.6-minimal_2.6.7-4_amd64.deb) ... Selecting previously unselected package python2.6. Unpacking python2.6 (from .../python2.6_2.6.7-4_amd64.deb) ... Selecting previously unselected package cython. Unpacking cython (from .../cython_0.15.1-2_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ... Selecting previously unselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26+nmu3_all.deb) ... Selecting previously unselected package xml-core. Unpacking xml-core (from .../xml-core_0.13+nmu1_all.deb) ... Selecting previously unselected package docutils-common. Unpacking docutils-common (from .../docutils-common_0.8.1-7_all.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-3_amd64.deb) ... Selecting previously unselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2.20110419-3_amd64.deb) ... Selecting previously unselected package libexpat1-dev. Unpacking libexpat1-dev (from .../libexpat1-dev_2.1.0-1_amd64.deb) ... Selecting previously unselected package libjs-jquery. Unpacking libjs-jquery (from .../libjs-jquery_1.7.2+debian-2_all.deb) ... Selecting previously unselected package libjs-underscore. Unpacking libjs-underscore (from .../libjs-underscore_1.3.3-1_all.deb) ... Selecting previously unselected package libjs-sphinxdoc. Unpacking libjs-sphinxdoc (from .../libjs-sphinxdoc_1.1.3+dfsg-4_all.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.1-3_amd64.deb) ... Selecting previously unselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.4.1-3_amd64.deb) ... Selecting previously unselected package libpython2.6. Unpacking libpython2.6 (from .../libpython2.6_2.6.7-4_amd64.deb) ... Selecting previously unselected package libpython2.7. Unpacking libpython2.7 (from .../libpython2.7_2.7.3-1_amd64.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ... Selecting previously unselected package libssl-dev. Unpacking libssl-dev (from .../libssl-dev_1.0.1c-3_amd64.deb) ... Selecting previously unselected package python-all. Unpacking python-all (from .../python-all_2.7.3~rc2-1_all.deb) ... Selecting previously unselected package python2.7-dev. Unpacking python2.7-dev (from .../python2.7-dev_2.7.3-1_amd64.deb) ... Selecting previously unselected package python-dev. Unpacking python-dev (from .../python-dev_2.7.3~rc2-1_all.deb) ... Selecting previously unselected package python2.6-dev. Unpacking python2.6-dev (from .../python2.6-dev_2.6.7-4_amd64.deb) ... Selecting previously unselected package python-all-dev. Unpacking python-all-dev (from .../python-all-dev_2.7.3~rc2-1_all.deb) ... Selecting previously unselected package python-roman. Unpacking python-roman (from .../python-roman_0.8.1-7_all.deb) ... Selecting previously unselected package python-docutils. Unpacking python-docutils (from .../python-docutils_0.8.1-7_all.deb) ... Selecting previously unselected package python-markupsafe. Unpacking python-markupsafe (from .../python-markupsafe_0.15-1_amd64.deb) ... Selecting previously unselected package python-jinja2. Unpacking python-jinja2 (from .../python-jinja2_2.6-1_amd64.deb) ... Selecting previously unselected package python-numpy. Unpacking python-numpy (from .../python-numpy_1%3a1.6.2-1_amd64.deb) ... Selecting previously unselected package python-pygments. Unpacking python-pygments (from .../python-pygments_1.5+dfsg-1_all.deb) ... Selecting previously unselected package sphinx-common. Unpacking sphinx-common (from .../sphinx-common_1.1.3+dfsg-4_all.deb) ... Selecting previously unselected package python-sphinx. Unpacking python-sphinx (from .../python-sphinx_1.1.3+dfsg-4_all.deb) ... Selecting previously unselected package sbuild-build-depends-python-cogent-dummy. Unpacking sbuild-build-depends-python-cogent-dummy (from .../sbuild-build-depends-python-cogent-dummy.deb) ... Setting up libncursesw5:amd64 (5.9-9) ... Setting up libpipeline1:amd64 (1.2.1-1) ... Setting up libssl1.0.0:amd64 (1.0.1c-3) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libmagic1:amd64 (5.11-1) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libsqlite3-0:amd64 (3.7.13-1) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libexpat1:amd64 (2.1.0-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up libgfortran3:amd64 (4.7.1-1) ... Setting up libdb4.8:amd64 (4.8.30-11) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-8) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-9) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.3-1) ... Setting up python2.7 (2.7.3-1) ... Setting up python-minimal (2.7.3~rc2-1) ... Setting up python (2.7.3~rc2-1) ... Setting up python-support (1.0.14) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up python2.6 (2.6.7-4) ... Setting up cython (0.15.1-2) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up sgml-base (1.26+nmu3) ... Updating the super catalog... Setting up xml-core (0.13+nmu1) ... Setting up libblas3 (1.2.20110419-3) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode. Setting up libblas3gf (1.2.20110419-3) ... Setting up libexpat1-dev (2.1.0-1) ... Setting up libjs-jquery (1.7.2+debian-2) ... Setting up libjs-underscore (1.3.3-1) ... Setting up libjs-sphinxdoc (1.1.3+dfsg-4) ... Setting up liblapack3 (3.4.1-3) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode. Setting up liblapack3gf (3.4.1-3) ... Setting up libpython2.6 (2.6.7-4) ... Setting up libpython2.7 (2.7.3-1) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up libssl-dev (1.0.1c-3) ... Setting up python-all (2.7.3~rc2-1) ... Setting up python2.7-dev (2.7.3-1) ... Setting up python-dev (2.7.3~rc2-1) ... Setting up python2.6-dev (2.6.7-4) ... Setting up python-all-dev (2.7.3~rc2-1) ... Setting up python-roman (0.8.1-7) ... Setting up python-markupsafe (0.15-1) ... Setting up python-jinja2 (2.6-1) ... Setting up python-numpy (1:1.6.2-1) ... Setting up python-pygments (1.5+dfsg-1) ... Setting up sphinx-common (1.1.3+dfsg-4) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up docutils-common (0.8.1-7) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up python-docutils (0.8.1-7) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode. Setting up python-sphinx (1.1.3+dfsg-4) ... Setting up sbuild-build-depends-python-cogent-dummy (0.invalid.0) ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc-4.6_4.6.3-7 gcc-4.7_4.7.1-1 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 linux-libc-dev_3.2.20-1 Package versions: apt_0.9.7 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 clang_3.1-6 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-7 cpp-4.7_4.7.1-1 cython_0.15.1-2 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffutils_1:3.2-6 docutils-common_0.8.1-7 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-1 findutils_4.4.2-4 g++_4:4.7.0-6 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc_4:4.7.0-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7_4.7.1-1 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-8 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblas3_1.2.20110419-3 libblas3gf_1.2.20110419-3 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclang-common-dev_3.1-6 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libgfortran3_4.7.1-1 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-1 libitm1_4.7.1-1 libjs-jquery_1.7.2+debian-2 libjs-sphinxdoc_1.1.3+dfsg-4 libjs-underscore_1.3.3-1 liblapack3_3.4.1-3 liblapack3gf_3.4.1-3 libllvm3.1_3.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-1 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-9 libncursesw5_5.9-9 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpython2.6_2.6.7-4 libpython2.7_2.7.3-1 libquadmath0_4.7.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libsqlite3-0_3.7.13-1 libss2_1.42.4-3 libssl-dev_1.0.1c-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.20-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-9 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3~rc2-1 python-all_2.7.3~rc2-1 python-all-dev_2.7.3~rc2-1 python-dev_2.7.3~rc2-1 python-docutils_0.8.1-7 python-jinja2_2.6-1 python-markupsafe_0.15-1 python-minimal_2.7.3~rc2-1 python-numpy_1:1.6.2-1 python-pygments_1.5+dfsg-1 python-roman_0.8.1-7 python-sphinx_1.1.3+dfsg-4 python-support_1.0.14 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.3-1 python2.7-dev_2.7.3-1 python2.7-minimal_2.7.3-1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-cogent-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu3 sphinx-common_1.1.3+dfsg-4 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xml-core_0.13+nmu1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sun Sep 4 09:55:07 2011 UTC using DSA key ID BE9D5339 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./python-cogent_1.5.1-2.dsc dpkg-source: info: extracting python-cogent in python-cogent-1.5.1 dpkg-source: info: unpacking python-cogent_1.5.1.orig.tar.gz dpkg-source: info: unpacking python-cogent_1.5.1-2.debian.tar.gz dpkg-source: info: applying fix_python_shebang_line.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-92ea38c6-5768-42f1-aaac-d75bcacfa32b SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package python-cogent dpkg-buildpackage: source version 1.5.1-2 dpkg-buildpackage: source changed by Steffen Moeller dpkg-source --before-build python-cogent-1.5.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 dh_testdir dh_auto_clean running clean 'build/lib.linux-x86_64-2.6' does not exist -- can't clean it 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-2.6' does not exist -- can't clean it running clean 'build/lib.linux-x86_64-2.7' does not exist -- can't clean it 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with python2 dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' cd doc; /usr/bin/make html make[2]: Entering directory `/«PKGBUILDDIR»/doc' sphinx-build -b html -d _build/doctrees . _build/html Making output directory... Running Sphinx v1.1.3 loading pickled environment... not yet created building [html]: targets for 97 source files that are out of date updating environment: 97 added, 0 changed, 0 removed reading sources... [ 1%] COGENT_LICENSE reading sources... [ 2%] ChangeLog reading sources... [ 3%] README reading sources... [ 4%] coding_guidelines reading sources... [ 5%] cookbook/DNA_and_RNA_sequences reading sources... [ 6%] cookbook/accessing_databases reading sources... [ 7%] cookbook/alignments reading sources... [ 8%] cookbook/alphabet reading sources... [ 9%] cookbook/analysis_of_sequence_composition reading sources... [ 10%] cookbook/annotations reading sources... [ 11%] cookbook/blast reading sources... [ 12%] cookbook/building_alignments reading sources... [ 13%] cookbook/building_phylogenies reading sources... [ 14%] cookbook/checkpointing_long_running reading sources... [ 15%] cookbook/code_development reading sources... [ 16%] cookbook/community_analysis reading sources... [ 17%] cookbook/controlling_third_party_applications reading sources... [ 18%] cookbook/dealing_with_hts_data reading sources... [ 19%] cookbook/ensembl reading sources... [ 20%] cookbook/genetic_code reading sources... [ 21%] cookbook/hpc_environments reading sources... [ 22%] cookbook/index reading sources... [ 23%] cookbook/introduction reading sources... [ 24%] cookbook/loading_sequences reading sources... [ 25%] cookbook/managing_trees reading sources... [ 26%] cookbook/manipulating_biological_data reading sources... [ 27%] cookbook/moltypesequence reading sources... [ 28%] cookbook/multivariate_data_analysis reading sources... [ 29%] cookbook/parallel_tasks reading sources... [ 30%] cookbook/phylonodes reading sources... [ 31%] cookbook/protein_sequences reading sources... [ 32%] cookbook/sequence_similarity_search reading sources... [ 34%] cookbook/sequence_simulation reading sources... [ 35%] cookbook/simple_trees reading sources... [ 36%] cookbook/standard_statistical_analyses reading sources... [ 37%] cookbook/structural_contacts reading sources... [ 38%] cookbook/structural_data reading sources... [ 39%] cookbook/structural_data_2 reading sources... [ 40%] cookbook/tables reading sources... [ 41%] cookbook/tips_for_using_python reading sources... [ 42%] cookbook/useful_utilities reading sources... [ 43%] cookbook/using_likelihood_to_perform_evolutionary_analyses reading sources... [ 44%] data_file_links reading sources... [ 45%] developer_notes reading sources... [ 46%] examples/align_codons_to_protein reading sources... [ 47%] examples/alignment_app_controllers reading sources... [ 48%] examples/aln_profile reading sources... [ 49%] examples/application_controller_framework reading sources... [ 50%] examples/building_and_using_an_application_controller reading sources... [ 51%] examples/calculate_UPGMA_cluster reading sources... [ 52%] examples/calculate_neigbourjoining_tree reading sources... [ 53%] examples/calculate_pairwise_distances reading sources... [ 54%] examples/codon_models reading sources... [ 55%] examples/coevolution reading sources... [ 56%] examples/complete_seq_features reading sources... [ 57%] examples/draw_dendrogram reading sources... [ 58%] examples/draw_dotplot reading sources... [ 59%] examples/empirical_protein_models reading sources... [ 60%] examples/entity_selection reading sources... [ 61%] examples/estimate_startingpoint reading sources... [ 62%] examples/generating_app_commandlines reading sources... [ 63%] examples/genetic_code_aa_index reading sources... [ 64%] examples/goodness_of_fit reading sources... [ 65%] examples/handling_3dstructures reading sources... [ 67%] examples/handling_tabular_data reading sources... [ 68%] examples/hmm_par_heterogeneity reading sources... [ 69%] examples/index reading sources... [ 70%] examples/maketree_from_proteinseqs reading sources... [ 71%] examples/manipulating_tree_nodes reading sources... [ 72%] examples/motif_results reading sources... [ 73%] examples/neutral_test reading sources... [ 74%] examples/parametric_bootstrap reading sources... [ 75%] examples/perform_PCoA_analysis reading sources... [ 76%] examples/perform_nmds reading sources... [ 77%] examples/period_estimation reading sources... [ 78%] examples/phylo_by_ls reading sources... [ 79%] examples/phylogeny_app_controllers reading sources... [ 80%] examples/query_ensembl reading sources... [ 81%] examples/query_ncbi reading sources... [ 82%] examples/rate_heterogeneity reading sources... [ 83%] examples/relative_rate reading sources... [ 84%] examples/reuse_results reading sources... [ 85%] examples/reverse_complement reading sources... [ 86%] examples/scope_model_params_on_trees reading sources... [ 87%] examples/seq_features reading sources... [ 88%] examples/seqsim_alignment_simulation reading sources... [ 89%] examples/seqsim_aln_sim_user_alphabet reading sources... [ 90%] examples/seqsim_tree_sim reading sources... [ 91%] examples/simple reading sources... [ 92%] examples/simulate_alignment reading sources... [ 93%] examples/testing_multi_loci reading sources... [ 94%] examples/translate_dna reading sources... [ 95%] examples/unifrac reading sources... [ 96%] examples/unrestricted_nucleotide reading sources... [ 97%] index reading sources... [ 98%] install reading sources... [100%] licenses looking for now-outdated files... none found pickling environment... done /«PKGBUILDDIR»/doc/cookbook/ensembl.rst:: WARNING: document isn't included in any toctree checking consistency... done preparing documents... done writing output... [ 1%] COGENT_LICENSE writing output... [ 2%] ChangeLog writing output... [ 3%] README writing output... [ 4%] coding_guidelines writing output... [ 5%] cookbook/DNA_and_RNA_sequences writing output... [ 6%] cookbook/accessing_databases writing output... [ 7%] cookbook/alignments writing output... [ 8%] cookbook/alphabet writing output... [ 9%] cookbook/analysis_of_sequence_composition writing output... [ 10%] cookbook/annotations writing output... [ 11%] cookbook/blast writing output... [ 12%] cookbook/building_alignments writing output... [ 13%] cookbook/building_phylogenies writing output... [ 14%] cookbook/checkpointing_long_running writing output... [ 15%] cookbook/code_development writing output... [ 16%] cookbook/community_analysis writing output... [ 17%] cookbook/controlling_third_party_applications writing output... [ 18%] cookbook/dealing_with_hts_data writing output... [ 19%] cookbook/ensembl writing output... [ 20%] cookbook/genetic_code writing output... [ 21%] cookbook/hpc_environments writing output... [ 22%] cookbook/index writing output... [ 23%] cookbook/introduction writing output... [ 24%] cookbook/loading_sequences writing output... [ 25%] cookbook/managing_trees writing output... [ 26%] cookbook/manipulating_biological_data writing output... [ 27%] cookbook/moltypesequence writing output... [ 28%] cookbook/multivariate_data_analysis writing output... [ 29%] cookbook/parallel_tasks writing output... [ 30%] cookbook/phylonodes writing output... [ 31%] cookbook/protein_sequences writing output... [ 32%] cookbook/sequence_similarity_search writing output... [ 34%] cookbook/sequence_simulation writing output... [ 35%] cookbook/simple_trees writing output... [ 36%] cookbook/standard_statistical_analyses writing output... [ 37%] cookbook/structural_contacts writing output... [ 38%] cookbook/structural_data writing output... [ 39%] cookbook/structural_data_2 writing output... [ 40%] cookbook/tables writing output... [ 41%] cookbook/tips_for_using_python writing output... [ 42%] cookbook/useful_utilities writing output... [ 43%] cookbook/using_likelihood_to_perform_evolutionary_analyses writing output... [ 44%] data_file_links writing output... [ 45%] developer_notes writing output... [ 46%] examples/align_codons_to_protein writing output... [ 47%] examples/alignment_app_controllers writing output... [ 48%] examples/aln_profile writing output... [ 49%] examples/application_controller_framework writing output... [ 50%] examples/building_and_using_an_application_controller writing output... [ 51%] examples/calculate_UPGMA_cluster writing output... [ 52%] examples/calculate_neigbourjoining_tree writing output... [ 53%] examples/calculate_pairwise_distances writing output... [ 54%] examples/codon_models writing output... [ 55%] examples/coevolution writing output... [ 56%] examples/complete_seq_features writing output... [ 57%] examples/draw_dendrogram writing output... [ 58%] examples/draw_dotplot writing output... [ 59%] examples/empirical_protein_models writing output... [ 60%] examples/entity_selection writing output... [ 61%] examples/estimate_startingpoint writing output... [ 62%] examples/generating_app_commandlines writing output... [ 63%] examples/genetic_code_aa_index writing output... [ 64%] examples/goodness_of_fit writing output... [ 65%] examples/handling_3dstructures writing output... [ 67%] examples/handling_tabular_data writing output... [ 68%] examples/hmm_par_heterogeneity writing output... [ 69%] examples/index writing output... [ 70%] examples/maketree_from_proteinseqs writing output... [ 71%] examples/manipulating_tree_nodes writing output... [ 72%] examples/motif_results writing output... [ 73%] examples/neutral_test writing output... [ 74%] examples/parametric_bootstrap writing output... [ 75%] examples/perform_PCoA_analysis writing output... [ 76%] examples/perform_nmds writing output... [ 77%] examples/period_estimation writing output... [ 78%] examples/phylo_by_ls writing output... [ 79%] examples/phylogeny_app_controllers writing output... [ 80%] examples/query_ensembl writing output... [ 81%] examples/query_ncbi writing output... [ 82%] examples/rate_heterogeneity writing output... [ 83%] examples/relative_rate WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting writing output... [ 84%] examples/reuse_results writing output... [ 85%] examples/reverse_complement writing output... [ 86%] examples/scope_model_params_on_trees writing output... [ 87%] examples/seq_features writing output... [ 88%] examples/seqsim_alignment_simulation writing output... [ 89%] examples/seqsim_aln_sim_user_alphabet writing output... [ 90%] examples/seqsim_tree_sim writing output... [ 91%] examples/simple writing output... [ 92%] examples/simulate_alignment writing output... [ 93%] examples/testing_multi_loci writing output... [ 94%] examples/translate_dna writing output... [ 95%] examples/unifrac writing output... [ 96%] examples/unrestricted_nucleotide writing output... [ 97%] index writing output... [ 98%] install writing output... [100%] licenses writing additional files... genindex search copying downloadable files... [ 6%] /«PKGBUILDDIR»/doc/data/motif_example.fasta copying downloadable files... [ 13%] /«PKGBUILDDIR»/doc/data/4TSV.pdb copying downloadable files... [ 20%] /«PKGBUILDDIR»/doc/cookbook/../data/long_testseqs.fasta copying downloadable files... [ 26%] /«PKGBUILDDIR»/doc/data/abglobin_aa.phylip copying downloadable files... [ 33%] /«PKGBUILDDIR»/doc/data/test.tree copying downloadable files... [ 40%] /«PKGBUILDDIR»/doc/data/test2.fasta copying downloadable files... [ 46%] /«PKGBUILDDIR»/doc/data/test.paml copying downloadable files... [ 53%] /«PKGBUILDDIR»/doc/data/trna_profile.fasta copying downloadable files... [ 60%] /«PKGBUILDDIR»/doc/data/primate_brca1.fasta copying downloadable files... [ 66%] /«PKGBUILDDIR»/doc/data/long_testseqs.fasta copying downloadable files... [ 73%] /«PKGBUILDDIR»/doc/data/primate_brca1.tree copying downloadable files... [ 80%] /«PKGBUILDDIR»/doc/data/dists_for_phylo.pickle copying downloadable files... [ 86%] /«PKGBUILDDIR»/doc/data/primate_cdx2_promoter.fasta copying downloadable files... [ 93%] /«PKGBUILDDIR»/doc/data/motif_example_meme_results.txt copying downloadable files... [100%] /«PKGBUILDDIR»/doc/../cogent-requirements.txt copying static files... done dumping search index... done dumping object inventory... done build succeeded, 2 warnings. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory `/«PKGBUILDDIR»/doc' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch --with python2 dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a running install running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/cogent copying cogent/__init__.py -> build/lib.linux-x86_64-2.6/cogent creating build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/dp_calculation.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/traceback.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/pycompare.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/progressive.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/partial_order_graph.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/pairwise.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/indel_positions.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/indel_model.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/align.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/algorithm.py -> build/lib.linux-x86_64-2.6/cogent/align copying cogent/align/__init__.py -> build/lib.linux-x86_64-2.6/cogent/align creating build/lib.linux-x86_64-2.6/cogent/align/weights copying cogent/align/weights/util.py -> build/lib.linux-x86_64-2.6/cogent/align/weights copying cogent/align/weights/methods.py -> build/lib.linux-x86_64-2.6/cogent/align/weights copying cogent/align/weights/__init__.py -> build/lib.linux-x86_64-2.6/cogent/align/weights creating build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/vienna_package.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/util.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/unafold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/uclust.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/stride.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/sfold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/sffinfo.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/sfffile.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rnaview.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rnashapes.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rnaforester.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rnaalifold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rdp_classifier20.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/rdp_classifier.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/raxml.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/pknotsrg.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/pfold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/parameters.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/nupack.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/muscle.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/msms.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/mothur.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/mfold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/mafft.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/knetfold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/infernal.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/ilm.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/gctmpca.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/formatdb.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/foldalign.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/fasttree_v1.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/fasttree.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/dynalign.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/dotur.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/dialign.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/cove.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/contrafold.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/consan.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/comrna.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/cmfinder.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/clustalw.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/clearcut.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/cd_hit.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/carnac.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/blast.py -> build/lib.linux-x86_64-2.6/cogent/app copying cogent/app/__init__.py -> build/lib.linux-x86_64-2.6/cogent/app creating build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/UPGMA.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/procrustes.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/nmds.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/metric_scaling.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/approximate_mds.py -> build/lib.linux-x86_64-2.6/cogent/cluster copying cogent/cluster/__init__.py -> build/lib.linux-x86_64-2.6/cogent/cluster creating build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/usage.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/tree.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/sequence.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/profile.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/moltype.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/location.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/info.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/genetic_code.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/entity.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/bitvector.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/annotation.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/alphabet.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/alignment.py -> build/lib.linux-x86_64-2.6/cogent/core copying cogent/core/__init__.py -> build/lib.linux-x86_64-2.6/cogent/core creating build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/molecular_weight.py -> build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/protein_properties.py -> build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/nucleic_properties.py -> build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/ligand_properties.py -> build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/energy_params.py -> build/lib.linux-x86_64-2.6/cogent/data copying cogent/data/__init__.py -> build/lib.linux-x86_64-2.6/cogent/data creating build/lib.linux-x86_64-2.6/cogent/db copying cogent/db/util.py -> build/lib.linux-x86_64-2.6/cogent/db copying cogent/db/rfam.py -> build/lib.linux-x86_64-2.6/cogent/db copying cogent/db/pdb.py -> build/lib.linux-x86_64-2.6/cogent/db copying cogent/db/ncbi.py -> build/lib.linux-x86_64-2.6/cogent/db copying cogent/db/__init__.py -> build/lib.linux-x86_64-2.6/cogent/db creating build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/util.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/species.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/region.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/name.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/host.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/database.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> build/lib.linux-x86_64-2.6/cogent/db/ensembl creating build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/util.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/rlg2mpl.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/multivariate_plot.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/linear.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/legend.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/fancy_arrow.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/dotplot.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/dinuc.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/dendrogram.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/compatibility.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/codon_usage.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/arrow_rates.py -> build/lib.linux-x86_64-2.6/cogent/draw copying cogent/draw/__init__.py -> build/lib.linux-x86_64-2.6/cogent/draw creating build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/substitution_model.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/substitution_calculation.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/solved_models.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/simulate.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/predicate.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/parameter_controller.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/pairwise_distance.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/motif_prob_model.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/models.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/likelihood_tree.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/likelihood_function.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/discrete_markov.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/coevolution.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/bootstrap.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/best_likelihood.py -> build/lib.linux-x86_64-2.6/cogent/evolve copying cogent/evolve/__init__.py -> build/lib.linux-x86_64-2.6/cogent/evolve creating build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/text_tree.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/xyzrn.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/table.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/structure.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/stockholm.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/rna_struct.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/phylip.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/pdb_color.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/pdb.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/nexus.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/motif.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/mage.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/fasta.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/clustal.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/alignment.py -> build/lib.linux-x86_64-2.6/cogent/format copying cogent/format/__init__.py -> build/lib.linux-x86_64-2.6/cogent/format creating build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/svd.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/solve.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/simannealingoptimiser.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/scipy_optimize.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/scipy_optimisers.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/period.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/optimisers.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/matrix_logarithm.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/matrix_exponentiation.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/markov.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/geometry.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/function_optimisation.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/fit_function.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/distance_transform.py -> build/lib.linux-x86_64-2.6/cogent/maths copying cogent/maths/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths creating build/lib.linux-x86_64-2.6/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> build/lib.linux-x86_64-2.6/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths/matrix creating build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/util.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/test.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/special.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/period.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/ks.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/kendall.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/histogram.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/distribution.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats copying cogent/maths/stats/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats creating build/lib.linux-x86_64-2.6/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths/stats/cai creating build/lib.linux-x86_64-2.6/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> build/lib.linux-x86_64-2.6/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> build/lib.linux-x86_64-2.6/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths/unifrac creating build/lib.linux-x86_64-2.6/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> build/lib.linux-x86_64-2.6/cogent/maths/spatial creating build/lib.linux-x86_64-2.6/cogent/motif copying cogent/motif/util.py -> build/lib.linux-x86_64-2.6/cogent/motif copying cogent/motif/k_word.py -> build/lib.linux-x86_64-2.6/cogent/motif copying cogent/motif/__init__.py -> build/lib.linux-x86_64-2.6/cogent/motif creating build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/unigene.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/unafold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/tree_xml.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/tree.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/tinyseq.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/table.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/structure.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/stride.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/stockholm.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/sprinzl.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/sfold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/sequence.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rnaview.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rnashapes.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rnaforester.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rnaalifold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rna_plot.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rna_fold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rfam.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/record_finder.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/record.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/rdb.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/psl.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/pknotsrg.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/phylip.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/pfold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/pdb.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/paml_matrix.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/paml.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/nupack.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/nexus.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/newick.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/msms.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/mothur.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/mfold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/meme.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/mage.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/macsim.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/locuslink.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/knetfold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/kegg_taxonomy.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/kegg_pos.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/kegg_ko.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/kegg_fasta.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/infernal.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/ilm.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/illumina_sequence.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/greengenes.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/gibbs.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/gff.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/genbank.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/gcg.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/gbseq.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/foldalign.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/flowgram_parser.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/flowgram_collection.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/flowgram.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/fastq.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/fasta.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/ebi.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/dynalign.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/dotur.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/dialign.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/cutg.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/cut.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/ct.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/cove.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/contrafold.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/consan.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/comrna.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/column.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/cmfinder.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/clustal.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/cigar.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/carnac.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/bpseq.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/bowtie.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/blast_xml.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/blast.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/binary_sff.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/agilent_microarray.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/aaindex.py -> build/lib.linux-x86_64-2.6/cogent/parse copying cogent/parse/__init__.py -> build/lib.linux-x86_64-2.6/cogent/parse creating build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/util.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/tree_space.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/tree_collection.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/nj.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/least_squares.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/distance.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/consensus.py -> build/lib.linux-x86_64-2.6/cogent/phylo copying cogent/phylo/__init__.py -> build/lib.linux-x86_64-2.6/cogent/phylo creating build/lib.linux-x86_64-2.6/cogent/recalculation copying cogent/recalculation/setting.py -> build/lib.linux-x86_64-2.6/cogent/recalculation copying cogent/recalculation/__init__.py -> build/lib.linux-x86_64-2.6/cogent/recalculation copying cogent/recalculation/scope.py -> build/lib.linux-x86_64-2.6/cogent/recalculation copying cogent/recalculation/definition.py -> build/lib.linux-x86_64-2.6/cogent/recalculation copying cogent/recalculation/calculation.py -> build/lib.linux-x86_64-2.6/cogent/recalculation creating build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/usage.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/tree.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/searchpath.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/randomization.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/microarray.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/markov.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/birth_death.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/analysis.py -> build/lib.linux-x86_64-2.6/cogent/seqsim copying cogent/seqsim/__init__.py -> build/lib.linux-x86_64-2.6/cogent/seqsim creating build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/selection.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/rna2d.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/pairs_util.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/manipulation.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/knots.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/dihedral.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/contact.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/asa.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/annotation.py -> build/lib.linux-x86_64-2.6/cogent/struct copying cogent/struct/__init__.py -> build/lib.linux-x86_64-2.6/cogent/struct creating build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/warning.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/update_version.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/unit_test.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/trie.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/transform.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/terminal.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/table.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/recode_alignment.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/progress_display.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/parallel.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/organizer.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/option_parsing.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/modules.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/misc.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/dict_array.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/dict2d.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/datatypes.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/checkpointing.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/array.py -> build/lib.linux-x86_64-2.6/cogent/util copying cogent/util/__init__.py -> build/lib.linux-x86_64-2.6/cogent/util running build_ext cythoning cogent/align/_compare.pyx to cogent/align/_compare.c building 'cogent.align._compare' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/cogent creating build/temp.linux-x86_64-2.6/cogent/align gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/align/_compare.c -o build/temp.linux-x86_64-2.6/cogent/align/_compare.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/align/_compare.o -o build/lib.linux-x86_64-2.6/cogent/align/_compare.so cythoning cogent/align/_pairwise_seqs.pyx to cogent/align/_pairwise_seqs.c building 'cogent.align._pairwise_seqs' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/align/_pairwise_seqs.c -o build/temp.linux-x86_64-2.6/cogent/align/_pairwise_seqs.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/align/_pairwise_seqs.o -o build/lib.linux-x86_64-2.6/cogent/align/_pairwise_seqs.so cythoning cogent/align/_pairwise_pogs.pyx to cogent/align/_pairwise_pogs.c building 'cogent.align._pairwise_pogs' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/align/_pairwise_pogs.c -o build/temp.linux-x86_64-2.6/cogent/align/_pairwise_pogs.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/align/_pairwise_pogs.o -o build/lib.linux-x86_64-2.6/cogent/align/_pairwise_pogs.so skipping 'cogent/evolve/_solved_models.c' Cython extension (up-to-date) building 'cogent.evolve._solved_models' extension creating build/temp.linux-x86_64-2.6/cogent/evolve gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/evolve/_solved_models.c -o build/temp.linux-x86_64-2.6/cogent/evolve/_solved_models.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/evolve/_solved_models.o -o build/lib.linux-x86_64-2.6/cogent/evolve/_solved_models.so cythoning cogent/evolve/_likelihood_tree.pyx to cogent/evolve/_likelihood_tree.c building 'cogent.evolve._likelihood_tree' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/evolve/_likelihood_tree.c -o build/temp.linux-x86_64-2.6/cogent/evolve/_likelihood_tree.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/evolve/_likelihood_tree.o -o build/lib.linux-x86_64-2.6/cogent/evolve/_likelihood_tree.so cythoning cogent/evolve/_pairwise_distance.pyx to cogent/evolve/_pairwise_distance.c building 'cogent.evolve._pairwise_distance' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/evolve/_pairwise_distance.c -o build/temp.linux-x86_64-2.6/cogent/evolve/_pairwise_distance.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/evolve/_pairwise_distance.o -o build/lib.linux-x86_64-2.6/cogent/evolve/_pairwise_distance.so cythoning cogent/struct/_asa.pyx to cogent/struct/_asa.c warning: cogent/struct/_asa.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.struct._asa' extension creating build/temp.linux-x86_64-2.6/cogent/struct gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/struct/_asa.c -o build/temp.linux-x86_64-2.6/cogent/struct/_asa.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/struct/_asa.o -o build/lib.linux-x86_64-2.6/cogent/struct/_asa.so cythoning cogent/struct/_contact.pyx to cogent/struct/_contact.c warning: cogent/struct/_contact.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.struct._contact' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/struct/_contact.c -o build/temp.linux-x86_64-2.6/cogent/struct/_contact.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/struct/_contact.o -o build/lib.linux-x86_64-2.6/cogent/struct/_contact.so skipping 'cogent/maths/_period.c' Cython extension (up-to-date) building 'cogent.maths._period' extension creating build/temp.linux-x86_64-2.6/cogent/maths gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/maths/_period.c -o build/temp.linux-x86_64-2.6/cogent/maths/_period.o -w gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/cogent/maths/_period.o -o build/lib.linux-x86_64-2.6/cogent/maths/_period.so cythoning cogent/maths/spatial/ckd3.pyx to cogent/maths/spatial/ckd3.c warning: cogent/maths/spatial/ckd3.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' building 'cogent.maths.spatial.ckd3' extension creating build/temp.linux-x86_64-2.6/cogent/maths/spatial gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/«PKGBUILDDIR»/include -I/usr/lib/pymodules/python2.6/numpy/core/include -I/usr/include/python2.6 -c cogent/maths/spatial/ckd3.c -o build/temp.linux-x86_64-2.6/cogent/maths/spatial/ckd3.o -w cogent/maths/spatial/ckd3.c:2847:3: error: non-void function '__pyx_pf_6cogent_5maths_7spatial_4ckd3_6KDTree___init__' should return a value [-Wreturn-type] import_array(); ^ /usr/lib/pymodules/python2.6/numpy/core/include/numpy/__multiarray_api.h:1616:144: note: expanded from macro 'import_array' #define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NUMPY_IMPORT_ARRAY_RETVAL; } } ^ 1 error generated. error: command 'gcc' failed with exit status 1 dh_auto_install: python2.6 setup.py install --force --root=/«PKGBUILDDIR»/debian/tmp --no-compile -O0 --install-layout=deb returned exit code 1 make: *** [binary-arch] Error 1 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1634 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 31312 Build-Time: 28 Distribution: unstable Fail-Stage: build Install-Time: 27 Job: python-cogent_1.5.1-2 Package: python-cogent Package-Time: 82 Source-Version: 1.5.1-2 Space: 31312 Status: attempted Version: 1.5.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1634 Build needed 00:01:22, 31312k disc space DC-Status: Failed 83.104794s