DC-Build-Header: python-biom-format 1.0.0-1 / Sat Feb 02 01:54:17 +0000 2013 DC-Task: logfile:/tmp/python-biom-format_1.0.0-1_unstable_clang.log version:1.0.0-1 modes:binary-only:clang chroot:unstable source:python-biom-format esttime: architecture:any DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang python-biom-format_1.0.0-1' Could not create '/sbuild-nonexistent/logs': No such file or directory Could not create '/sbuild-nonexistent/logs': No such file or directory sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-157-6-66.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ python-biom-format 1.0.0-1 (amd64) 02 Feb 2013 01:54 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: python-biom-format Version: 1.0.0-1 Source Version: 1.0.0-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-biom-format-7Ucio0/python-biom-format-1.0.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/python-biom-format-7Ucio0' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-cdd79a4d-281c-42ad-a043-8bc29a7f2e3a' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [227 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Get:3 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:4 http://localhost unstable/main 2013-02-01-2012.11.pdiff [40 B] Get:5 http://localhost unstable/main 2013-02-01-2012.11.pdiff [40 B] Get:6 http://localhost unstable/main Sources [8235 kB] Get:7 http://localhost unstable/main amd64 Packages [8278 kB] Fetched 16.7 MB in 3s (4958 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: 'python-biom-format' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ Need to get 116 kB of source archives. Get:1 http://localhost/debian/ unstable/main python-biom-format 1.0.0-1 (dsc) [1472 B] Get:2 http://localhost/debian/ unstable/main python-biom-format 1.0.0-1 (tar) [77.6 kB] Get:3 http://localhost/debian/ unstable/main python-biom-format 1.0.0-1 (diff) [37.1 kB] Fetched 116 kB in 0s (610 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... + echo 'Add an unstable version of clang as repository' Add an unstable version of clang as repository + echo deb http://clang.ecranbleu.org/apt/debian unstable main + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Ign http://localhost unstable/main Sources/DiffIndex Ign http://clang.ecranbleu.org unstable InRelease Ign http://localhost unstable/main amd64 Packages/DiffIndex Ign http://clang.ecranbleu.org unstable Release.gpg Hit http://localhost unstable/main Translation-en/DiffIndex Get:1 http://clang.ecranbleu.org unstable Release [1616 B] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Get:2 http://clang.ecranbleu.org unstable/main amd64 Packages [2354 B] Ign http://clang.ecranbleu.org unstable/main Translation-en Fetched 3970 B in 1s (2022 B/s) 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 Ign http://localhost unstable/main Sources/DiffIndex Ign http://clang.ecranbleu.org unstable InRelease Ign http://localhost unstable/main amd64 Packages/DiffIndex Ign http://clang.ecranbleu.org unstable Release.gpg Hit http://localhost unstable/main Translation-en/DiffIndex Hit http://clang.ecranbleu.org unstable Release Ign http://clang.ecranbleu.org unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Hit http://clang.ecranbleu.org unstable/main amd64 Packages Ign http://clang.ecranbleu.org unstable/main Translation-en Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: clang-3.2 compiler-rt libclang-common-dev libexpat1 libffi5 libllvm3.2 libncursesw5 libsqlite3-0 libssl1.0.0 mime-support python python-minimal python2.7 python2.7-minimal Suggested packages: python-doc python-tk python2.7-doc binfmt-support Recommended packages: llvm-3.2-dev file The following NEW packages will be installed: clang clang-3.2 compiler-rt libclang-common-dev libexpat1 libffi5 libllvm3.2 libncursesw5 libsqlite3-0 libssl1.0.0 mime-support python python-minimal python2.7 python2.7-minimal 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. Need to get 25.3 MB of archives. After this operation, 70.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libclang-common-dev compiler-rt clang-3.2 clang Get:1 http://localhost/debian/ unstable/main libncursesw5 amd64 5.9-10 [141 kB] Get:2 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-4 [1213 kB] Get:3 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.15.2-1 [463 kB] Get:4 http://localhost/debian/ unstable/main libexpat1 amd64 2.1.0-1 [141 kB] Get:5 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:6 http://localhost/debian/ unstable/main libllvm3.2 amd64 3.2-2 [7865 kB] Get:7 http://localhost/debian/ unstable/main mime-support all 3.52-2 [35.2 kB] Get:8 http://localhost/debian/ unstable/main python2.7-minimal amd64 2.7.3-6 [1783 kB] Get:9 http://localhost/debian/ unstable/main python2.7 amd64 2.7.3-6 [2729 kB] Get:10 http://clang.ecranbleu.org/apt/debian/ unstable/main libclang-common-dev amd64 3.2-2 [303 kB] Get:11 http://localhost/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB] Get:12 http://localhost/debian/ unstable/main python all 2.7.3-3 [179 kB] Get:13 http://clang.ecranbleu.org/apt/debian/ unstable/main compiler-rt amd64 3.2-2 [312 kB] Get:14 http://clang.ecranbleu.org/apt/debian/ unstable/main clang-3.2 amd64 3.2-2 [10.0 MB] Get:15 http://clang.ecranbleu.org/apt/debian/ unstable/main clang all 3.2-2 [9558 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.3 MB in 9s (2776 kB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 13484 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-10_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-4_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.15.2-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.2:amd64. Unpacking libllvm3.2:amd64 (from .../libllvm3.2_3.2-2_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-6_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-6_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-3_all.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.2-2_amd64.deb) ... Selecting previously unselected package compiler-rt. Unpacking compiler-rt (from .../compiler-rt_3.2-2_amd64.deb) ... Selecting previously unselected package clang-3.2. Unpacking clang-3.2 (from .../clang-3.2_3.2-2_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.2-2_all.deb) ... Setting up libncursesw5:amd64 (5.9-10) ... Setting up libssl1.0.0:amd64 (1.0.1c-4) ... 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 Setting up libsqlite3-0:amd64 (3.7.15.2-1) ... Setting up libexpat1:amd64 (2.1.0-1) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.2:amd64 (3.2-2) ... Setting up mime-support (3.52-2) ... Setting up python2.7-minimal (2.7.3-6) ... Linking and byte-compiling packages for runtime python2.7... Setting up python2.7 (2.7.3-6) ... Setting up python-minimal (2.7.3-3) ... Setting up python (2.7.3-3) ... Setting up libclang-common-dev (3.2-2) ... Setting up compiler-rt (3.2-2) ... Setting up clang-3.2 (3.2-2) ... Setting up clang (3.2-2) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7' + cd /usr/bin + for VERSION in '$VERSIONS' + rm g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + 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 + 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' + dpkg --set-selections + 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/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-eg5XCP/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/710 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 ... 14662 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, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), python-all-dev (>= 2.6), python-numpy, cython Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), python-all-dev (>= 2.6), python-numpy, cython dpkg-deb: building package `sbuild-build-depends-python-biom-format-dummy' in `/«BUILDDIR»/resolver-GONmMA/apt_archive/sbuild-build-depends-python-biom-format-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install python-biom-format 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 file gettext gettext-base groff-base html2text intltool-debian libasprintf-dev libasprintf0c2 libblas3 libblas3gf libcroco3 libexpat1-dev libgettextpo-dev libgettextpo0 libgfortran3 libglib2.0-0 liblapack3 liblapack3gf libmagic1 libpcre3 libpipeline1 libpython2.6 libpython2.7 libssl-dev libunistring0 libxml2 man-db po-debconf python-all python-all-dev python-dev python-numpy python-support python2.6 python2.6-dev python2.6-minimal python2.7-dev zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python-numpy-doc python-numpy-dbg python-nose gfortran python2.6-doc binfmt-support Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info libssl-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cython debhelper file gettext gettext-base groff-base html2text intltool-debian libasprintf-dev libasprintf0c2 libblas3 libblas3gf libcroco3 libexpat1-dev libgettextpo-dev libgettextpo0 libgfortran3 libglib2.0-0 liblapack3 liblapack3gf libmagic1 libpcre3 libpipeline1 libpython2.6 libpython2.7 libssl-dev libunistring0 libxml2 man-db po-debconf python-all python-all-dev python-dev python-numpy python-support python2.6 python2.6-dev python2.6-minimal python2.7-dev sbuild-build-depends-python-biom-format-dummy zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 55.3 MB/55.3 MB of archives. After this operation, 128 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.2-1 [39.9 kB] Get:2 http://localhost/debian/ unstable/main groff-base amd64 1.22.1-2 [741 kB] Get:3 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.4 [210 kB] Get:4 http://localhost/debian/ unstable/main man-db amd64 2.6.3-3 [898 kB] Get:5 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-10 [27.2 kB] Get:6 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-2 [202 kB] Get:7 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.31-2 [247 kB] Get:8 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-7 [903 kB] Get:9 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.33.12+really2.32.4-5 [1838 kB] Get:10 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.6-2 [134 kB] Get:11 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:12 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-10 [145 kB] Get:13 http://localhost/debian/ unstable/main libgfortran3 amd64 4.7.2-5 [351 kB] Get:14 http://localhost/debian/ unstable/main file amd64 5.11-2 [51.8 kB] Get:15 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-10 [154 kB] Get:16 http://localhost/debian/ unstable/main python-support all 1.0.15 [33.6 kB] Get:17 http://localhost/debian/ unstable/main python2.6-minimal amd64 2.6.8-1.1 [1547 kB] Get:18 http://localhost/debian/ unstable/main cython amd64 0.15.1-2 [1923 kB] Get:19 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:20 http://localhost/debian/ unstable/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB] Get:21 http://localhost/debian/ unstable/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB] Get:22 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-10 [1815 kB] Get:23 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:24 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:25 http://localhost/debian/ unstable/main debhelper all 9.20120909 [705 kB] Get:26 http://localhost/debian/ unstable/main libblas3 amd64 1.2.20110419-5 [293 kB] Get:27 http://localhost/debian/ unstable/main libblas3gf all 1.2.20110419-5 [8090 B] Get:28 http://localhost/debian/ unstable/main libexpat1-dev amd64 2.1.0-1 [229 kB] Get:29 http://localhost/debian/ unstable/main liblapack3 amd64 3.4.1-6 [5036 kB] Get:30 http://localhost/debian/ unstable/main liblapack3gf all 3.4.1-6 [10.2 kB] Get:31 http://localhost/debian/ unstable/main python2.6 amd64 2.6.8-1.1 [2509 kB] Get:32 http://localhost/debian/ unstable/main libpython2.6 amd64 2.6.8-1.1 [1104 kB] Get:33 http://localhost/debian/ unstable/main libpython2.7 amd64 2.7.3-6 [1208 kB] Get:34 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] Get:35 http://localhost/debian/ unstable/main libssl-dev amd64 1.0.1c-4 [1698 kB] Get:36 http://localhost/debian/ unstable/main python-all all 2.7.3-3 [876 B] Get:37 http://localhost/debian/ unstable/main python2.7-dev amd64 2.7.3-6 [22.8 MB] Get:38 http://localhost/debian/ unstable/main python-dev all 2.7.3-3 [916 B] Get:39 http://localhost/debian/ unstable/main python2.6-dev amd64 2.6.8-1.1 [4577 kB] Get:40 http://localhost/debian/ unstable/main python-all-dev all 2.7.3-3 [894 B] Get:41 http://localhost/debian/ unstable/main python-numpy amd64 1:1.6.2-1 [2631 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.3 MB in 1s (32.2 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14662 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-1_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.1-2_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-2_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_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.7.2-5_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_amd64.deb) ... 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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_9.20120909_all.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2.20110419-5_all.deb) ... Selecting previously unselected package libexpat1-dev. Unpacking libexpat1-dev (from .../libexpat1-dev_2.1.0-1_amd64.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.1-6_amd64.deb) ... Selecting previously unselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.4.1-6_all.deb) ... Selecting previously unselected package python2.6. Unpacking python2.6 (from .../python2.6_2.6.8-1.1_amd64.deb) ... Selecting previously unselected package libpython2.6. Unpacking libpython2.6 (from .../libpython2.6_2.6.8-1.1_amd64.deb) ... Selecting previously unselected package libpython2.7. Unpacking libpython2.7 (from .../libpython2.7_2.7.3-6_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-4_amd64.deb) ... Selecting previously unselected package python-all. Unpacking python-all (from .../python-all_2.7.3-3_all.deb) ... Selecting previously unselected package python2.7-dev. Unpacking python2.7-dev (from .../python2.7-dev_2.7.3-6_amd64.deb) ... Selecting previously unselected package python-dev. Unpacking python-dev (from .../python-dev_2.7.3-3_all.deb) ... Selecting previously unselected package python2.6-dev. Unpacking python2.6-dev (from .../python2.6-dev_2.6.8-1.1_amd64.deb) ... Selecting previously unselected package python-all-dev. Unpacking python-all-dev (from .../python-all-dev_2.7.3-3_all.deb) ... Selecting previously unselected package python-numpy. Unpacking python-numpy (from .../python-numpy_1%3a1.6.2-1_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-python-biom-format-dummy. Unpacking sbuild-build-depends-python-biom-format-dummy (from .../sbuild-build-depends-python-biom-format-dummy.deb) ... Processing triggers for mime-support ... Setting up libpipeline1:amd64 (1.2.2-1) ... Setting up groff-base (1.22.1-2) ... Setting up bsdmainutils (9.0.4) ... 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 man-db (2.6.3-3) ... Building database of manual pages ... Setting up libasprintf0c2:amd64 (0.18.1.1-10) ... Setting up libmagic1:amd64 (5.11-2) ... Setting up libpcre3:amd64 (1:8.31-2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.6-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-10) ... Setting up libgfortran3:amd64 (4.7.2-5) ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-10) ... Setting up python-support (1.0.15) ... Setting up python2.6-minimal (2.6.8-1.1) ... Setting up cython (0.15.1-2) ... Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Setting up libblas3 (1.2.20110419-5) ... 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 (1.2.20110419-5) ... Setting up libexpat1-dev (2.1.0-1) ... Setting up liblapack3 (3.4.1-6) ... 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 (3.4.1-6) ... Setting up python2.6 (2.6.8-1.1) ... Setting up libpython2.6 (2.6.8-1.1) ... Setting up libpython2.7 (2.7.3-6) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up libssl-dev (1.0.1c-4) ... Setting up python-all (2.7.3-3) ... Setting up python2.7-dev (2.7.3-6) ... Setting up python-dev (2.7.3-3) ... Setting up python2.6-dev (2.6.8-1.1) ... Setting up python-all-dev (2.7.3-3) ... Setting up python-numpy (1:1.6.2-1) ... Setting up sbuild-build-depends-python-biom-format-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_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 g++-4.7_4.7.2-5 gcc-4.6_4.6.3-15 gcc-4.7_4.7.2-5 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-5 linux-libc-dev_3.2.35-2 Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 clang_3.2-2 clang-3.2_3.2-2 compiler-rt_3.2-2 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.6_4.6.3-15 cpp-4.7_4.7.2-5 cython_0.15.1-2 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.7.2-1 g++-4.6_4.6.3-15 g++-4.7_4.7.2-5 gcc_4:4.7.2-1 gcc-4.4-base_4.4.7-3 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7_4.7.2-5 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.1-2 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-39 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblas3_1.2.20110419-5 libblas3gf_1.2.20110419-5 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclang-common-dev_3.2-2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libgfortran3_4.7.2-5 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 libgpm2_1.20.4-6 libitm1_4.7.2-5 liblapack3_3.4.1-6 liblapack3gf_3.4.1-6 libllvm3.2_3.2-2 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 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_1:8.31-2 libpipeline1_1.2.2-1 libpython2.6_2.6.8-1.1 libpython2.7_2.7.3-6 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.15.2-1 libss2_1.42.5-1 libssl-dev_1.0.1c-4 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-5 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_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-17 perl-base_5.14.2-17 perl-modules_5.14.2-17 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-all_2.7.3-3 python-all-dev_2.7.3-3 python-dev_2.7.3-3 python-minimal_2.7.3-3 python-numpy_1:1.6.2-1 python-support_1.0.15 python2.6_2.6.8-1.1 python2.6-dev_2.6.8-1.1 python2.6-minimal_2.6.8-1.1 python2.7_2.7.3-6 python2.7-dev_2.7.3-6 python2.7-minimal_2.7.3-6 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biom-format-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-39 sysvinit_2.88dsf-39 sysvinit-utils_2.88dsf-39 tar_1.26+dfsg-0.1 tzdata_2012j-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.3 vim_2:7.3.547-6 vim-common_2:7.3.547-6 vim-runtime_2:7.3.547-6 xz-utils_5.1.1alpha+20120614-2 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 Fri Aug 3 14:02:51 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./python-biom-format_1.0.0-1.dsc dpkg-source: info: extracting python-biom-format in python-biom-format-1.0.0 dpkg-source: info: unpacking python-biom-format_1.0.0.orig.tar.gz dpkg-source: info: unpacking python-biom-format_1.0.0-1.debian.tar.gz dpkg-source: info: applying enable_cython_beta.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-cdd79a4d-281c-42ad-a043-8bc29a7f2e3a SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package python-biom-format dpkg-buildpackage: source version 1.0.0-1 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build python-biom-format-1.0.0 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 # ,sphinxdoc dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' 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 rm -rf python-code/support-code/_sparsemat.cpp make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch --with python2 # ,sphinxdoc dh_testdir -a dh_auto_configure -a dh_auto_build -a running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/biom copying python-code/biom/__init__.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/util.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/sparsemat.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/sparsedict.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/unit_test.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/exception.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/parse.py -> build/lib.linux-x86_64-2.6/biom copying python-code/biom/table.py -> build/lib.linux-x86_64-2.6/biom running build_ext building 'biom._sparsemat' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/python-code creating build/temp.linux-x86_64-2.6/python-code/support-code gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.6 -c python-code/support-code/_sparsemat.cpp -o build/temp.linux-x86_64-2.6/python-code/support-code/_sparsemat.o gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.6 -c python-code/support-code/sparsemat_lib.cpp -o build/temp.linux-x86_64-2.6/python-code/support-code/sparsemat_lib.o In file included from python-code/support-code/sparsemat_lib.cpp:2: python-code/support-code/sparsemat_lib.h:17:37: error: use of undeclared identifier 'uint64_t' typedef std::tr1::unordered_map float_map_t; ^ python-code/support-code/sparsemat_lib.h:18:37: error: use of undeclared identifier 'uint64_t' typedef std::tr1::unordered_map int_map_t; ^ python-code/support-code/sparsemat_lib.h:22:9: error: unknown type name 'uint32_t' uint32_t *rows; ^ python-code/support-code/sparsemat_lib.h:23:9: error: unknown type name 'uint32_t' uint32_t *cols; ^ python-code/support-code/sparsemat_lib.h:24:9: error: unknown type name 'int32_t'; did you mean '__int32_t'? int32_t *values; ^~~~~~~ __int32_t /usr/include/x86_64-linux-gnu/bits/types.h:41:20: note: '__int32_t' declared here typedef signed int __int32_t; ^ In file included from python-code/support-code/sparsemat_lib.cpp:2: python-code/support-code/sparsemat_lib.h:28:9: error: unknown type name 'uint32_t' uint32_t *rows; ^ python-code/support-code/sparsemat_lib.h:29:9: error: unknown type name 'uint32_t' uint32_t *cols; ^ python-code/support-code/sparsemat_lib.h:36:13: error: unknown type name 'uint64_t' uint64_t current_key; ^ python-code/support-code/sparsemat_lib.h:42:25: error: unknown type name 'uint32_t' void insert(uint32_t row, uint32_t col, double value); ^ python-code/support-code/sparsemat_lib.h:42:39: error: unknown type name 'uint32_t' void insert(uint32_t row, uint32_t col, double value); ^ python-code/support-code/sparsemat_lib.h:43:24: error: unknown type name 'uint32_t' double get(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:43:38: error: unknown type name 'uint32_t' double get(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:44:24: error: unknown type name 'uint32_t' void erase(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:44:38: error: unknown type name 'uint32_t' void erase(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:45:26: error: unknown type name 'uint32_t' int contains(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:45:40: error: unknown type name 'uint32_t' int contains(uint32_t row, uint32_t col); ^ python-code/support-code/sparsemat_lib.h:46:13: error: unknown type name 'uint32_t' uint32_t length(); ^ python-code/support-code/sparsemat_lib.h:55:13: error: unknown type name 'uint64_t' uint64_t current_key; ^ python-code/support-code/sparsemat_lib.h:61:25: error: unknown type name 'uint32_t' void insert(uint32_t row, uint32_t col, int32_t value); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. error: command 'gcc' failed with exit status 1 dh_auto_build: python2.6 setup.py build --force returned exit code 1 make: *** [build-arch] Error 1 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130202-0155 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 1860 Build-Time: 5 Distribution: unstable Fail-Stage: build Install-Time: 14 Job: python-biom-format_1.0.0-1 Package: python-biom-format Package-Time: 50 Source-Version: 1.0.0-1 Space: 1860 Status: attempted Version: 1.0.0-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130202-0155 Build needed 00:00:50, 1860k disc space DC-Status: Failed 51.240519s DC-Time-Estimation: 51.240519 versus expected 1 (r/m: 50.240519 ; m: 1.0)