DC-Build-Header: python-biom-format 1.2.0-1 / 2014-01-06 09:01:57 +0000 DC-Task: source:python-biom-format version:1.2.0-1 architecture:any chroot:unstable esttime:44 logfile:/tmp/python-biom-format_1.2.0-1_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " python-biom-format_1.2.0-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-10-169.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ python-biom-format 1.2.0-1clang1 (amd64) 06 Jan 2014 09:01 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: python-biom-format Version: 1.2.0-1clang1 Source Version: 1.2.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/python-biom-format-Ojl_nl/python-biom-format-1.2.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/python-biom-format-Ojl_nl' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-3c0d928e-189f-4b93-a764-665fd2f65cef' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [206 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 2014-01-04-1439.27.pdiff [11.3 kB] Get:6 http://localhost:9999 unstable/main 2014-01-04-1439.27.pdiff [11.3 kB] Get:7 http://localhost:9999 unstable/main amd64 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http://localhost:9999 unstable/main amd64 2014-01-06-0239.34.pdiff [21.1 kB] Get:46 http://localhost:9999 unstable/main 2014-01-06-0239.34.pdiff [238 B] Fetched 412 kB in 28s (14.6 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: libterm-ui-perl 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.1 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libterm-ui-perl all 0.42-1 [19.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.1 kB in 0s (1191 kB/s) (Reading database ... 13944 files and directories currently installed.) Preparing to unpack .../libterm-ui-perl_0.42-1_all.deb ... Unpacking libterm-ui-perl (0.42-1) over (0.38-1) ... Setting up libterm-ui-perl (0.42-1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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-biom-format' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ Need to get 5658 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main python-biom-format 1.2.0-1 (dsc) [1524 B] Get:2 http://localhost:9999/debian/ unstable/main python-biom-format 1.2.0-1 (tar) [5651 kB] Get:3 http://localhost:9999/debian/ unstable/main python-biom-format 1.2.0-1 (diff) [5380 B] Fetched 5658 kB in 2s (2646 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-3.4' Install of clang-3.4 + 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-3.4 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.8-dev libobjc4 Recommended packages: llvm-3.4-dev python The following NEW packages will be installed: clang-3.4 libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.8-dev libobjc4 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 82.1 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.0.13-10 [19.3 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.4 amd64 1:3.4-1 [6528 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.8.2-11 [110 kB] Get:4 http://localhost:9999/debian/ unstable/main libobjc-4.8-dev amd64 4.8.2-11 [370 kB] Get:5 http://localhost:9999/debian/ unstable/main libclang1-3.4 amd64 1:3.4-1 [3526 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.4-dev amd64 1:3.4-1 [516 kB] Get:7 http://localhost:9999/debian/ unstable/main clang-3.4 amd64 1:3.4-1 [8878 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (25.7 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 13944 files and directories currently installed.) Preparing to unpack .../libffi6_3.0.13-10_amd64.deb ... Unpacking libffi6:amd64 (3.0.13-10) ... Selecting previously unselected package libllvm3.4:amd64. Preparing to unpack .../libllvm3.4_1%3a3.4-1_amd64.deb ... Unpacking libllvm3.4:amd64 (1:3.4-1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.8.2-11_amd64.deb ... Unpacking libobjc4:amd64 (4.8.2-11) ... Selecting previously unselected package libobjc-4.8-dev:amd64. Preparing to unpack .../libobjc-4.8-dev_4.8.2-11_amd64.deb ... Unpacking libobjc-4.8-dev:amd64 (4.8.2-11) ... Selecting previously unselected package libclang1-3.4:amd64. Preparing to unpack .../libclang1-3.4_1%3a3.4-1_amd64.deb ... Unpacking libclang1-3.4:amd64 (1:3.4-1) ... Selecting previously unselected package libclang-common-3.4-dev. Preparing to unpack .../libclang-common-3.4-dev_1%3a3.4-1_amd64.deb ... Unpacking libclang-common-3.4-dev (1:3.4-1) ... Selecting previously unselected package clang-3.4. Preparing to unpack .../clang-3.4_1%3a3.4-1_amd64.deb ... Unpacking clang-3.4 (1:3.4-1) ... Setting up libffi6:amd64 (3.0.13-10) ... Setting up libllvm3.4:amd64 (1:3.4-1) ... Setting up libobjc4:amd64 (4.8.2-11) ... Setting up libobjc-4.8-dev:amd64 (4.8.2-11) ... Setting up libclang1-3.4:amd64 (1:3.4-1) ... Setting up libclang-common-3.4-dev (1:3.4-1) ... Setting up clang-3.4 (1:3.4-1) ... Processing triggers for libc-bin (2.17-97) ... + 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-FeLMD3/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/766 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 ... 14105 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, 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, python-numpy, cython (>= 0.17), help2man, python-dateutil, python-cogent, pyqi, python-nose 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, python-numpy, cython (>= 0.17), help2man, python-dateutil, python-cogent, pyqi, python-nose dpkg-deb: building package `sbuild-build-depends-python-biom-format-dummy' in `/«BUILDDIR»/resolver-0hJnbS/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 help2man 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 pyqi python python-all python-all-dev python-cogent python-dateutil python-dev python-minimal python-nose python-numpy python-pkg-resources 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-cogent-doc python-coverage python-nose-doc python-numpy-doc python-numpy-dbg gfortran python-distribute python-distribute-doc 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 help2man 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 pyqi python python-all python-all-dev python-cogent python-dateutil python-dev python-minimal python-nose python-numpy python-pkg-resources python-support python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-python-biom-format-dummy 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 44.1 MB/44.1 MB of archives. After this operation, 112 MB of additional disk space will be used. 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(Reading database ... 14105 files and directories currently installed.) Preparing to unpack .../libncursesw5_5.9+20130608-1_amd64.deb ... Unpacking libncursesw5:amd64 (5.9+20130608-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.2.6-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.2.6-1) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1e-6_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1e-6) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-3_amd64.deb ... Unpacking groff-base (1.22.2-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ... Unpacking bsdmainutils (9.0.5) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.5-3_amd64.deb ... Unpacking man-db (2.6.5-3) ... Selecting previously unselected package libasprintf0c2:amd64. 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Preparing to unpack .../sbuild-build-depends-python-biom-format-dummy.deb ... Unpacking sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ... Setting up libncursesw5:amd64 (5.9+20130608-1) ... Setting up libpipeline1:amd64 (1.2.6-1) ... Setting up libssl1.0.0:amd64 (1.0.1e-6) ... 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 (2.6.5-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3.1-2) ... Setting up libmagic1:amd64 (1:5.14-2) ... Setting up libsqlite3-0:amd64 (3.8.2-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3) ... Setting up libglib2.0-0:amd64 (2.36.4-1) ... 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 (4.8.2-11) ... Setting up libpython2.7-minimal:amd64 (2.7.6-4) ... Setting up mime-support (3.54) ... Setting up libpython2.7-stdlib:amd64 (2.7.6-4) ... Setting up libpython2.7:amd64 (2.7.6-4) ... Setting up libexpat1-dev:amd64 (2.1.0-4) ... Setting up libpython2.7-dev:amd64 (2.7.6-4) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up python2.7-minimal (2.7.6-4) ... Setting up file (1:5.14-2) ... Setting up gettext-base (0.18.3.1-2) ... Setting up python2.7 (2.7.6-4) ... Setting up python-minimal (2.7.5-5) ... Setting up libpython-stdlib:amd64 (2.7.5-5) ... Setting up python (2.7.5-5) ... Setting up python-support (1.0.15) ... Setting up cython (0.19.2+git5-g0c6fdf0-1) ... Setting up gettext (0.18.3.1-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20131227) ... Setting up help2man (1.43.3) ... Setting up libblas3 (1.2.20110419-7) ... 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 (3.5.0-2) ... 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 (2.7.5-5) ... Setting up libpython-all-dev:amd64 (2.7.5-5) ... Setting up pyqi (0.2.0-2) ... Setting up python-all (2.7.5-5) ... Setting up python2.7-dev (2.7.6-4) ... Setting up python-dev (2.7.5-5) ... Setting up python-all-dev (2.7.5-5) ... Setting up python-dateutil (1.5+dfsg-0.1) ... Setting up python-pkg-resources (2.0.2-1) ... Setting up python-nose (1.3.0-2.1) ... Setting up python-numpy (1:1.7.1-3) ... Setting up python-cogent (1.5.3-2) ... Setting up sbuild-build-depends-python-biom-format-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.17-97) ... Processing triggers for python-support (1.0.15) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24-2 dpkg-dev_1.17.5 g++-4.6_4.6.4-5 g++-4.8_4.8.2-11 gcc-4.6_4.6.4-5 gcc-4.7_4.7.3-9 gcc-4.8_4.8.2-11 libc6-dev_2.17-97 libstdc++-4.8-dev_4.8.2-11 libstdc++6_4.8.2-11 libstdc++6-4.6-dev_4.6.4-5 linux-libc-dev_3.12.6-2 Package versions: apt_0.9.14.2 base-files_7.2 base-passwd_3.5.29 bash_4.2+dfsg-1 binutils_2.24-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 clang-3.4_1:3.4-1 coreutils_8.21-1 cpp_4:4.8.2-1 cpp-4.6_4.6.4-5 cpp-4.7_4.7.3-9 cpp-4.8_4.8.2-11 cython_0.19.2+git5-g0c6fdf0-1 dash_0.5.7-3+nmu1 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131227 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.5 dpkg-dev_1.17.5 e2fslibs_1.42.9-2 e2fsprogs_1.42.9-2 fakeroot_1.20-3 file_1:5.14-2 findutils_4.4.2-7 g++_4:4.8.2-1 g++-4.6_4.6.4-5 g++-4.8_4.8.2-11 gcc_4:4.8.2-1 gcc-4.4-base_4.4.7-6 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-5 gcc-4.6-base_4.6.4-5 gcc-4.7_4.7.3-9 gcc-4.7-base_4.7.3-9 gcc-4.8_4.8.2-11 gcc-4.8-base_4.8.2-11 gettext_0.18.3.1-2 gettext-base_0.18.3.1-2 gnupg_1.4.15-3 gpgv_1.4.15-3 grep_2.15-2 groff-base_1.22.2-3 gzip_1.6-3 help2man_1.43.3 hostname_3.15 initscripts_2.88dsf-45 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.14.2 libarchive-extract-perl_0.70-1 libasan0_4.8.2-11 libasprintf0c2_0.18.3.1-2 libatomic1_4.8.2-11 libattr1_1:2.4.47-1 libaudit-common_1:2.3.2-3 libaudit1_1:2.3.2-3 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libc-bin_2.17-97 libc-dev-bin_2.17-97 libc6_2.17-97 libc6-dev_2.17-97 libcap2_1:2.22-1.2 libclang-common-3.4-dev_1:3.4-1 libclang1-3.4_1:3.4-1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.1-3 libcloog-ppl1_0.16.1-4 libcomerr2_1.42.9-2 libcroco3_0.6.8-2 libdb5.1_5.1.29-7 libdpkg-perl_1.17.5 libexpat1_2.1.0-4 libexpat1-dev_2.1.0-4 libfakeroot_1.20-3 libffi6_3.0.13-10 libfile-fcntllock-perl_0.14-2+b1 libgc1c2_1:7.2d-6 libgcc-4.7-dev_4.7.3-9 libgcc-4.8-dev_4.8.2-11 libgcc1_1:4.8.2-11 libgdbm3_1.8.3-12 libgfortran3_4.8.2-11 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.3+dfsg-1 libgmpxx4ldbl_2:5.1.3+dfsg-1 libgomp1_4.8.2-11 libgpm2_1.20.4-6.1 libisl10_0.12.1-2 libitm1_4.8.2-11 liblapack3_3.5.0-2 libllvm3.4_1:3.4-1 liblocale-gettext-perl_1.05-7+b2 liblog-message-simple-perl_0.10-1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmodule-pluggable-perl_4.8-1 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libobjc-4.8-dev_4.8.2-11 libobjc4_4.8.2-11 libpam-modules_1.1.3-10 libpam-modules-bin_1.1.3-10 libpam-runtime_1.1.3-10 libpam0g_1.1.3-10 libpcre3_1:8.31-2 libpipeline1_1.2.6-1 libpod-latex-perl_0.61-1 libppl-c4_1:1.0-7 libppl12_1:1.0-7 libpython-all-dev_2.7.5-5 libpython-dev_2.7.5-5 libpython-stdlib_2.7.5-5 libpython2.7_2.7.6-4 libpython2.7-dev_2.7.6-4 libpython2.7-minimal_2.7.6-4 libpython2.7-stdlib_2.7.6-4 libquadmath0_4.8.2-11 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.1-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsqlite3-0_3.8.2-1 libss2_1.42.9-2 libssl1.0.0_1.0.1e-6 libstdc++-4.8-dev_4.8.2-11 libstdc++6_4.8.2-11 libstdc++6-4.6-dev_4.6.4-5 libswitch-perl_2.16-2 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-soundex-perl_3.4-1+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-1 libtinfo5_5.9+20130608-1 libtsan0_4.8.2-11 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.12.6-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 make_3.81-8.3 man-db_2.6.5-3 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.5 multiarch-support_2.17-97 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.1-5 perl-base_5.18.1-5 perl-modules_5.18.1-5 po-debconf_1.0.16+nmu2 pyqi_0.2.0-2 python_2.7.5-5 python-all_2.7.5-5 python-all-dev_2.7.5-5 python-cogent_1.5.3-2 python-dateutil_1.5+dfsg-0.1 python-dev_2.7.5-5 python-minimal_2.7.5-5 python-nose_1.3.0-2.1 python-numpy_1:1.7.1-3 python-pkg-resources_2.0.2-1 python-support_1.0.15 python2.7_2.7.6-4 python2.7-dev_2.7.6-4 python2.7-minimal_2.7.6-4 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_4.2.2-3 sensible-utils_0.0.9 sudo_1.8.8-2 sysv-rc_2.88dsf-45 sysvinit_2.88dsf-45 sysvinit-core_2.88dsf-45 sysvinit-utils_2.88dsf-45 tar_1.27-4 tzdata_2013i-1 ucf_3.0027+nmu1 util-linux_2.20.1-5.5 vim_2:7.4.052-1 vim-common_2:7.4.052-1 vim-runtime_2:7.4.052-1 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 Thu Nov 14 08:41:08 2013 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_1.2.0-1.dsc dpkg-source: info: extracting python-biom-format in python-biom-format-1.2.0 dpkg-source: info: unpacking python-biom-format_1.2.0.orig.tar.gz dpkg-source: info: unpacking python-biom-format_1.2.0-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 1.2.0-1clang1 User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-3c0d928e-189f-4b93-a764-665fd2f65cef SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package python-biom-format dpkg-buildpackage: source version 1.2.0-1clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build python-biom-format-1.2.0 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»' rm -rf build/tests dh_auto_clean 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 find -name "._*" -exec rm -f '{}' ';' #Needed if you try to build from pristine tarball 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_64-2.7 creating 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/unit_test.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/table.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/parse.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/csmat.py -> build/lib.linux-x86_64-2.7/biom copying python-code/biom/__init__.py -> build/lib.linux-x86_64-2.7/biom creating build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/table_validator.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/table_summarizer.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/table_subsetter.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/table_converter.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/metadata_adder.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/installation_informer.py -> build/lib.linux-x86_64-2.7/biom/commands copying python-code/biom/commands/__init__.py -> build/lib.linux-x86_64-2.7/biom/commands creating build/lib.linux-x86_64-2.7/biom/interfaces copying python-code/biom/interfaces/__init__.py -> build/lib.linux-x86_64-2.7/biom/interfaces creating build/lib.linux-x86_64-2.7/biom/interfaces/optparse copying python-code/biom/interfaces/optparse/output_handler.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse copying python-code/biom/interfaces/optparse/input_handler.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse copying python-code/biom/interfaces/optparse/__init__.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse creating build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/validate_table.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/summarize_table.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/subset_table.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/show_install_info.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/convert.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/add_metadata.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config copying python-code/biom/interfaces/optparse/config/__init__.py -> build/lib.linux-x86_64-2.7/biom/interfaces/optparse/config 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 python-code/support-code/_sparsemat.cpp:6831:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { ^ python-code/support-code/_sparsemat.cpp:6828:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) { ^ python-code/support-code/_sparsemat.cpp:359:29: warning: unused function '__Pyx_Py_UNICODE_strlen' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) ^ python-code/support-code/_sparsemat.cpp:6887:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6945:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ python-code/support-code/_sparsemat.cpp:6958:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:5809:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ python-code/support-code/_sparsemat.cpp:6061:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6080:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6099:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6118:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6137:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6175:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6194:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6213:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6232:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6439:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ python-code/support-code/_sparsemat.cpp:6561:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 18 warnings generated. 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 20140106-0903 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 35648 Build-Time: 9 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 30 Job: python-biom-format_1.2.0-1 Machine Architecture: amd64 Package: python-biom-format Package-Time: 91 Source-Version: 1.2.0-1 Space: 35648 Status: attempted Version: 1.2.0-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140106-0903 Build needed 00:01:31, 35648k disc space DC-Status: Failed 92.56652325s DC-Time-Estimation: 92.56652325 versus expected 44 (r/m: 1.103784619318182 ; m: 44.0)