DC-Build-Header: python-biom-format 1.0.0-1 / 2013-07-18 10:45:56 +0000 DC-Task: source:python-biom-format version:1.0.0-1 architecture:any chroot:unstable esttime:44 logfile:/tmp/python-biom-format_1.0.0-1_unstable_clang.log modes:binary-only:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " python-biom-format_1.0.0-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-10-235-5-15.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ python-biom-format 1.0.0-1clang1 (amd64) 18 Jul 2013 10:45 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: python-biom-format Version: 1.0.0-1clang1 Source Version: 1.0.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-biom-format-gF646v/python-biom-format-1.0.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/python-biom-format-gF646v' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-e78c99d7-1c4b-49d7-9984-f6163061fa42' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [204 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:6 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:7 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] 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Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt cpp-4.7 cpp-4.8 g++-4.8 gcc-4.7 gcc-4.7-base gcc-4.8 gcc-4.8-base initscripts libapt-pkg4.12 libasan0 libatomic1 libgcc-4.7-dev libgcc-4.8-dev libgcc1 libgomp1 libitm1 libquadmath0 libstdc++-4.8-dev libstdc++6 libtsan0 linux-libc-dev sysv-rc sysvinit sysvinit-utils 25 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 44.5 MB of archives. After this operation, 47.1 kB of additional disk space will be used. 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Setting up apt (0.9.9.2) ... gpg: key B98321F9: "Squeeze Stable Release Key " not changed gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) " not changed gpg: key 65FFB764: "Wheezy Stable Release Key " not changed gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysv-rc 2.88dsf-41 (using .../sysv-rc_2.88dsf-43_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace sysvinit-utils 2.88dsf-41 (using .../sysvinit-utils_2.88dsf-43_amd64.deb) ... Unpacking replacement sysvinit-utils ... Setting up sysvinit-utils (2.88dsf-43) ... Setting up sysv-rc (2.88dsf-43) ... (Reading database ... 13844 files and directories currently installed.) Preparing to replace initscripts 2.88dsf-41 (using .../initscripts_2.88dsf-43_amd64.deb) ... Removing unmodified and obsolete conffile /etc/init.d/mtab.sh ... Unpacking replacement initscripts ... Setting up initscripts (2.88dsf-43) ... Installing new version of config file /etc/init.d/bootmisc.sh ... Installing new version of config file /etc/init.d/checkfs.sh ... Installing new version of config file /etc/init.d/checkroot.sh ... Installing new version of config file /etc/init.d/checkroot-bootclean.sh ... Installing new version of config file /etc/init.d/mountdevsubfs.sh ... Installing new version of config file /etc/init.d/mountkernfs.sh ... Installing new version of config file /etc/init.d/rmnologin ... Installing new version of config file /etc/network/if-up.d/mountnfs ... (Reading database ... 13843 files and directories currently installed.) Preparing to replace gcc-4.7 4.7.3-5 (using .../gcc-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.3-5 (using .../cpp-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement cpp-4.7 ... 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Setting up gcc-4.7 (4.7.3-6) ... Setting up linux-libc-dev:amd64 (3.10.1-1) ... Processing triggers for libc-bin ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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:9999/debian/ unstable/main python-biom-format 1.0.0-1 (dsc) [1472 B] Get:2 http://localhost:9999/debian/ unstable/main python-biom-format 1.0.0-1 (tar) [77.6 kB] Get:3 http://localhost:9999/debian/ unstable/main python-biom-format 1.0.0-1 (diff) [37.1 kB] Fetched 116 kB in 0s (527 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 'Install of clang' Install of clang + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.3 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev Suggested packages: libstdc++6-4.7-doc Recommended packages: llvm-3.3-dev python The following NEW packages will be installed: clang-3.3 libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After this operation, 80.8 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.0.13-4 [21.6 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.3 amd64 1:3.3-3 [8575 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.8.1-7 [160 kB] Get:4 http://localhost:9999/debian/ unstable/main libstdc++6-4.7-dev amd64 4.7.3-6 [1694 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc-4.7-dev amd64 4.7.3-6 [719 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.3-dev amd64 1:3.3-3 [574 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.3 amd64 1:3.3-3 [4579 kB] Get:8 http://localhost:9999/debian/ unstable/main clang-3.3 amd64 1:3.3-3 [10.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.2 MB in 1s (25.7 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 13846 files and directories currently installed.) Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ... Selecting previously unselected package libllvm3.3:amd64. Unpacking libllvm3.3:amd64 (from .../libllvm3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8.1-7_amd64.deb) ... Selecting previously unselected package libstdc++6-4.7-dev:amd64. Unpacking libstdc++6-4.7-dev:amd64 (from .../libstdc++6-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libclang-common-3.3-dev. Unpacking libclang-common-3.3-dev (from .../libclang-common-3.3-dev_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libclang1-3.3. Unpacking libclang1-3.3 (from .../libclang1-3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package clang-3.3. Unpacking clang-3.3 (from .../clang-3.3_1%3a3.3-3_amd64.deb) ... Setting up libffi6:amd64 (3.0.13-4) ... Setting up libllvm3.3:amd64 (1:3.3-3) ... Setting up libobjc4:amd64 (4.8.1-7) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.3-6) ... Setting up libobjc-4.7-dev:amd64 (4.7.3-6) ... Setting up libclang-common-3.3-dev (1:3.3-3) ... Setting up libclang1-3.3 (1:3.3-3) ... Setting up clang-3.3 (1:3.3-3) ... Processing triggers for libc-bin ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm -f 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + 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' + dpkg --set-selections + echo 'gcc-4.8 hold' + dpkg --set-selections + echo 'cpp-4.8 hold' + dpkg --set-selections + echo 'g++-4.8 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version + grep clang + cpp --version + grep clang + g++ --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-aoGIJk/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 ... 14701 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-FXSH_p/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 intltool-debian libasprintf0c2 libblas3 libcroco3 libexpat1 libexpat1-dev libgfortran3 libglib2.0-0 liblapack3 libmagic1 libncursesw5 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-numpy python-support python2.7 python2.7-dev python2.7-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python-doc python-tk python-numpy-doc python-numpy-dbg python-nose gfortran python2.7-doc binfmt-support Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cython debhelper file gettext gettext-base groff-base intltool-debian libasprintf0c2 libblas3 libcroco3 libexpat1 libexpat1-dev libgfortran3 libglib2.0-0 liblapack3 libmagic1 libncursesw5 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-numpy python-support python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-python-biom-format-dummy 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 50.6 MB/50.6 MB of archives. After this operation, 110 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libncursesw5 amd64 5.9+20130608-1 [141 kB] Get:2 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.2.4-1 [41.0 kB] Get:3 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1e-3 [1242 kB] Get:4 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-3 [747 kB] Get:5 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:6 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.5-2 [976 kB] Get:7 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.3-1 [29.6 kB] Get:8 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.14-2 [216 kB] Get:9 http://localhost:9999/debian/ unstable/main libsqlite3-0 amd64 3.7.17-1 [478 kB] Get:10 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-2 [911 kB] Get:11 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.36.3-3 [2048 kB] Get:12 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:13 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-4 [138 kB] Get:14 http://localhost:9999/debian/ unstable/main libgfortran3 amd64 4.8.1-7 [345 kB] Get:15 http://localhost:9999/debian/ unstable/main libpython2.7-minimal amd64 2.7.5-6 [520 kB] Get:16 http://localhost:9999/debian/ unstable/main mime-support all 3.54 [36.4 kB] Get:17 http://localhost:9999/debian/ unstable/main libpython2.7-stdlib amd64 2.7.5-6 [2482 kB] Get:18 http://localhost:9999/debian/ unstable/main libpython2.7 amd64 2.7.5-6 [1361 kB] Get:19 http://localhost:9999/debian/ unstable/main libexpat1-dev amd64 2.1.0-4 [223 kB] Get:20 http://localhost:9999/debian/ unstable/main libpython2.7-dev amd64 2.7.5-6 [23.5 MB] Get:21 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:22 http://localhost:9999/debian/ unstable/main python2.7-minimal amd64 2.7.5-6 [1552 kB] Get:23 http://localhost:9999/debian/ unstable/main file amd64 1:5.14-2 [54.0 kB] Get:24 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.3-1 [161 kB] Get:25 http://localhost:9999/debian/ unstable/main python2.7 amd64 2.7.5-6 [229 kB] Get:26 http://localhost:9999/debian/ unstable/main python-minimal amd64 2.7.5-2 [42.7 kB] Get:27 http://localhost:9999/debian/ unstable/main libpython-stdlib amd64 2.7.5-2 [19.6 kB] Get:28 http://localhost:9999/debian/ unstable/main python amd64 2.7.5-2 [186 kB] Get:29 http://localhost:9999/debian/ unstable/main python-support all 1.0.15 [33.6 kB] Get:30 http://localhost:9999/debian/ unstable/main cython amd64 0.19+git51-g3078752-2 [1526 kB] Get:31 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.3-1 [1898 kB] Get:32 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:33 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:34 http://localhost:9999/debian/ unstable/main debhelper all 9.20130630 [710 kB] Get:35 http://localhost:9999/debian/ unstable/main libblas3 amd64 1.2.20110419-5 [293 kB] Get:36 http://localhost:9999/debian/ unstable/main liblapack3 amd64 3.4.2+dfsg-1 [5088 kB] Get:37 http://localhost:9999/debian/ unstable/main libpython-dev amd64 2.7.5-2 [19.6 kB] Get:38 http://localhost:9999/debian/ unstable/main libpython-all-dev amd64 2.7.5-2 [900 B] Get:39 http://localhost:9999/debian/ unstable/main python-all amd64 2.7.5-2 [870 B] Get:40 http://localhost:9999/debian/ unstable/main python2.7-dev amd64 2.7.5-6 [288 kB] Get:41 http://localhost:9999/debian/ unstable/main python-dev amd64 2.7.5-2 [1068 B] Get:42 http://localhost:9999/debian/ unstable/main python-all-dev amd64 2.7.5-2 [890 B] Get:43 http://localhost:9999/debian/ unstable/main python-numpy amd64 1:1.7.1-2 [2013 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.6 MB in 2s (20.5 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 14701 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130608-1_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1e-3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.3-1_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.17-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-2_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.36.3-3_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-4_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.8.1-7_amd64.deb) ... Selecting previously unselected package libpython2.7-minimal. Unpacking libpython2.7-minimal (from .../libpython2.7-minimal_2.7.5-6_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.54_all.deb) ... Selecting previously unselected package libpython2.7-stdlib. Unpacking libpython2.7-stdlib (from .../libpython2.7-stdlib_2.7.5-6_amd64.deb) ... Selecting previously unselected package libpython2.7. Unpacking libpython2.7 (from .../libpython2.7_2.7.5-6_amd64.deb) ... Selecting previously unselected package libexpat1-dev:amd64. Unpacking libexpat1-dev:amd64 (from .../libexpat1-dev_2.1.0-4_amd64.deb) ... Selecting previously unselected package libpython2.7-dev. Unpacking libpython2.7-dev (from .../libpython2.7-dev_2.7.5-6_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.5-6_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.3-1_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.5-6_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.5-2_amd64.deb) ... Selecting previously unselected package libpython-stdlib:amd64. Unpacking libpython-stdlib:amd64 (from .../libpython-stdlib_2.7.5-2_amd64.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.5-2_amd64.deb) ... Selecting previously unselected package python-support. Unpacking python-support (from .../python-support_1.0.15_all.deb) ... Selecting previously unselected package cython. Unpacking cython (from .../cython_0.19+git51-g3078752-2_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.3-1_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_9.20130630_all.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.2+dfsg-1_amd64.deb) ... Selecting previously unselected package libpython-dev:amd64. Unpacking libpython-dev:amd64 (from .../libpython-dev_2.7.5-2_amd64.deb) ... Selecting previously unselected package libpython-all-dev:amd64. Unpacking libpython-all-dev:amd64 (from .../libpython-all-dev_2.7.5-2_amd64.deb) ... Selecting previously unselected package python-all. Unpacking python-all (from .../python-all_2.7.5-2_amd64.deb) ... Selecting previously unselected package python2.7-dev. Unpacking python2.7-dev (from .../python2.7-dev_2.7.5-6_amd64.deb) ... Selecting previously unselected package python-dev. Unpacking python-dev (from .../python-dev_2.7.5-2_amd64.deb) ... Selecting previously unselected package python-all-dev. Unpacking python-all-dev (from .../python-all-dev_2.7.5-2_amd64.deb) ... Selecting previously unselected package python-numpy. Unpacking python-numpy (from .../python-numpy_1%3a1.7.1-2_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) ... Setting up libncursesw5:amd64 (5.9+20130608-1) ... Setting up libpipeline1:amd64 (1.2.4-1) ... Setting up libssl1.0.0:amd64 (1.0.1e-3) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5) ... 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 (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3-1) ... Setting up libmagic1:amd64 (1:5.14-2) ... Setting up libsqlite3-0:amd64 (3.7.17-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-2) ... Setting up libglib2.0-0:amd64 (2.36.3-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libexpat1:amd64 (2.1.0-4) ... Setting up libgfortran3:amd64 (4.8.1-7) ... Setting up libpython2.7-minimal (2.7.5-6) ... Setting up mime-support (3.54) ... Setting up libpython2.7-stdlib (2.7.5-6) ... Setting up libpython2.7 (2.7.5-6) ... Setting up libexpat1-dev:amd64 (2.1.0-4) ... Setting up libpython2.7-dev (2.7.5-6) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up python2.7-minimal (2.7.5-6) ... Setting up file (1:5.14-2) ... Setting up gettext-base (0.18.3-1) ... Setting up python2.7 (2.7.5-6) ... Setting up python-minimal (2.7.5-2) ... Setting up libpython-stdlib:amd64 (2.7.5-2) ... Setting up python (2.7.5-2) ... Setting up python-support (1.0.15) ... Setting up cython (0.19+git51-g3078752-2) ... Setting up gettext (0.18.3-1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20130630) ... 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 liblapack3 (3.4.2+dfsg-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpython-dev:amd64 (2.7.5-2) ... Setting up libpython-all-dev:amd64 (2.7.5-2) ... Setting up python-all (2.7.5-2) ... Setting up python2.7-dev (2.7.5-6) ... Setting up python-dev (2.7.5-2) ... Setting up python-all-dev (2.7.5-2) ... Setting up python-numpy (1:1.7.1-2) ... Setting up sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ... Processing triggers for libc-bin ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.23.52.20130620-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-4 g++-4.8_4.8.1-7 gcc-4.6_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.8_4.8.1-7 libc6-dev_2.17-7 libstdc++-4.8-dev_4.8.1-7 libstdc++6_4.8.1-7 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 linux-libc-dev_3.10.1-1 Package versions: apt_0.9.9.2 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130620-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-4 clang-3.3_1:3.3-3 coreutils_8.20-3 cpp_4:4.8.1-2 cpp-4.6_4.6.4-4 cpp-4.7_4.7.3-6 cpp-4.8_4.8.1-7 cython_0.19+git51-g3078752-2 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debian-archive-keyring_2012.4 debianutils_4.3.4 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.19-2 file_1:5.14-2 findutils_4.4.2-6 g++_4:4.8.1-2 g++-4.6_4.6.4-4 g++-4.8_4.8.1-7 gcc_4:4.8.1-2 gcc-4.4-base_4.4.7-4 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-4 gcc-4.6-base_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.7-base_4.7.3-6 gcc-4.8_4.8.1-7 gcc-4.8-base_4.8.1-7 gettext_0.18.3-1 gettext-base_0.18.3-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 hostname_3.13 initscripts_2.88dsf-43 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.9.2 libasan0_4.8.1-7 libasprintf0c2_0.18.3-1 libatomic1_4.8.1-7 libattr1_1:2.4.47-1 libblas3_1.2.20110419-5 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-4 libc-bin_2.17-7 libc-dev-bin_2.17-7 libc6_2.17-7 libc6-dev_2.17-7 libcap2_1:2.22-1.2 libclang-common-3.3-dev_1:3.3-3 libclang1-3.3_1:3.3-3 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcloog-ppl1_0.16.1-3 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdpkg-perl_1.16.10 libexpat1_2.1.0-4 libexpat1-dev_2.1.0-4 libffi6_3.0.13-4 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.2d-5 libgcc-4.7-dev_4.7.3-6 libgcc-4.8-dev_4.8.1-7 libgcc1_1:4.8.1-7 libgdbm3_1.8.3-12 libgfortran3_4.8.1-7 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-2 libgmpxx4ldbl_2:5.1.2+dfsg-2 libgomp1_4.8.1-7 libgpm2_1.20.4-6.1 libisl10_0.11.2-1 libitm1_4.8.1-7 liblapack3_3.4.2+dfsg-1 libllvm3.3_1:3.3-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libobjc-4.7-dev_4.7.3-6 libobjc4_4.8.1-7 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libppl-c4_1:1.0-7 libppl12_1:1.0-7 libpython-all-dev_2.7.5-2 libpython-dev_2.7.5-2 libpython-stdlib_2.7.5-2 libpython2.7_2.7.5-6 libpython2.7-dev_2.7.5-6 libpython2.7-minimal_2.7.5-6 libpython2.7-stdlib_2.7.5-6 libquadmath0_4.8.1-7 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libslang2_2.2.4-15 libsqlite3-0_3.7.17-1 libss2_1.42.8-1 libssl1.0.0_1.0.1e-3 libstdc++-4.8-dev_4.8.1-7 libstdc++6_4.8.1-7 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 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+20130608-1 libtsan0_4.8.1-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-2 linux-libc-dev_3.10.1-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 make_3.81-8.2 man-db_2.6.5-2 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.5 multiarch-support_2.17-7 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.14.2-21 perl-base_5.14.2-21 perl-modules_5.14.2-21 po-debconf_1.0.16+nmu2 python_2.7.5-2 python-all_2.7.5-2 python-all-dev_2.7.5-2 python-dev_2.7.5-2 python-minimal_2.7.5-2 python-numpy_1:1.7.1-2 python-support_1.0.15 python2.7_2.7.5-6 python2.7-dev_2.7.5-6 python2.7-minimal_2.7.5-6 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_4.2.2-1 sensible-utils_0.0.9 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-6 tzdata_2013c-2 ucf_3.0027+nmu1 util-linux_2.20.1-5.5 vim_2:7.3.923-3 vim-common_2:7.3.923-3 vim-runtime_2:7.3.923-3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 Hack binNMU version ─────────────────── Created changelog entry for binNMU version 1.0.0-1clang1 User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-e78c99d7-1c4b-49d7-9984-f6163061fa42 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package python-biom-format dpkg-buildpackage: source version 1.0.0-1clang1 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 pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions pyversions: missing debian/pyversions file, fall back to supported versions 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 pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions pyversions: missing debian/pyversions file, fall back to supported versions running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/biom copying python-code/biom/__init__.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/util.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/sparsemat.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/sparsedict.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/unit_test.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/exception.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/parse.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/table.py -> build/lib.linux-x86_64-2.7/biom running build_ext building 'biom._sparsemat' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/python-code creating build/temp.linux-x86_64-2.7/python-code/support-code x86_64-linux-gnu-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/python2.7 -c python-code/support-code/_sparsemat.cpp -o build/temp.linux-x86_64-2.7/python-code/support-code/_sparsemat.o x86_64-linux-gnu-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/python2.7 -c python-code/support-code/sparsemat_lib.cpp -o build/temp.linux-x86_64-2.7/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:40:20: 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 'x86_64-linux-gnu-gcc' failed with exit status 1 dh_auto_build: python 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 20130718-1048 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 1908 Build-Time: 8 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 19 Job: python-biom-format_1.0.0-1 Machine Architecture: amd64 Package: python-biom-format Package-Time: 124 Source-Version: 1.0.0-1 Space: 1908 Status: attempted Version: 1.0.0-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130718-1048 Build needed 00:02:04, 1908k disc space DC-Status: Failed 125.096118402s DC-Time-Estimation: 125.096118402 versus expected 44 (r/m: 1.8430936000454545 ; m: 44.0)