DC-Build-Header: ncbi-blast+ 2.2.27-3 / Mon Jan 28 04:07:46 +0000 2013 DC-Task: logfile:/tmp/ncbi-blast+_2.2.27-3_unstable_clang.log version:2.2.27-3 chroot:unstable modes:binary-only:clang source:ncbi-blast+ architecture:any esttime:10762 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang ncbi-blast+_2.2.27-3' 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-10-30-130-26.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ ncbi-blast+ 2.2.27-3 (amd64) 28 Jan 2013 04:07 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: ncbi-blast+ Version: 2.2.27-3 Source Version: 2.2.27-3 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/ncbi-blast+-2ZgS7v' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-248a94f5-6bfd-469d-8e2e-d938670141e9' 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 2013-01-27-2011.16.pdiff [737 B] Get:5 http://localhost unstable/main 2013-01-27-2011.16.pdiff [737 B] Get:6 http://localhost unstable/main Sources [8234 kB] Get:7 http://localhost unstable/main amd64 Packages [8284 kB] Fetched 16.8 MB in 3s (4932 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: 'ncbi-blast+' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/ Need to get 13.1 MB of source archives. Get:1 http://localhost/debian/ unstable/main ncbi-blast+ 2.2.27-3 (dsc) [2316 B] Get:2 http://localhost/debian/ unstable/main ncbi-blast+ 2.2.27-3 (tar) [13.0 MB] Get:3 http://localhost/debian/ unstable/main ncbi-blast+ 2.2.27-3 (diff) [22.9 kB] Fetched 13.1 MB in 1s (12.3 MB/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 experimental as repository' Add experimental as repository + echo deb http://localhost:9999/debian experimental main + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Get:1 http://localhost experimental Release.gpg [836 B] Hit http://localhost unstable Release Get:2 http://localhost experimental Release [161 kB] Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Get:3 http://localhost experimental/main Translation-en [704 kB] Get:4 http://localhost experimental/main amd64 Packages [1605 kB] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Fetched 2471 kB in 1s (1306 kB/s) Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Ign http://localhost experimental InRelease Hit http://localhost unstable Release.gpg Hit http://localhost experimental Release.gpg Hit http://localhost unstable Release Hit http://localhost experimental Release Ign http://localhost unstable/main Sources/DiffIndex Ign http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Ign http://localhost experimental/main amd64 Packages/DiffIndex Get:1 http://localhost experimental/main Translation-en/DiffIndex [7819 B] Hit http://localhost unstable/main Sources Hit http://localhost unstable/main amd64 Packages Hit http://localhost experimental/main amd64 Packages Fetched 7819 B in 1s (3960 B/s) Reading package lists... + apt-get install --yes --no-install-recommends clang -t experimental Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: clang-3.2 compiler-rt cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base gcc-4.8-base libc-dev-bin libc6 libc6-dev libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libgcc1 libgomp1 libitm1 libllvm3.2 libncurses5 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsqlite3-0 libssl1.0.0 libstdc++6 libstdc++6-4.7-dev libtinfo5 mime-support python python-minimal python2.7 python2.7-minimal Suggested packages: gcc-4.7-locales g++-4.7-multilib gcc-4.7-doc libstdc++6-4.7-dbg gcc-4.7-multilib libmudflap0-4.7-dev libgcc1-dbg libgomp1-dbg libitm1-dbg libquadmath0-dbg libmudflap0-dbg libcloog-ppl0 libppl-c2 libppl7 binutils-gold glibc-doc libstdc++6-4.7-doc python-doc python-tk python2.7-doc binfmt-support Recommended packages: llvm-3.2-dev manpages-dev file The following NEW packages will be installed: clang clang-3.2 compiler-rt gcc-4.8-base libclang-common-dev libexpat1 libffi5 libgcc-4.7-dev libllvm3.2 libncursesw5 libobjc-4.7-dev libobjc4 libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support python python-minimal python2.7 python2.7-minimal The following packages will be upgraded: cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libitm1 libncurses5 libquadmath0 libstdc++6 libstdc++6-4.7-dev libtinfo5 15 upgraded, 21 newly installed, 0 to remove and 24 not upgraded. Need to get 56.7 MB of archives. After this operation, 72.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ experimental/main gcc-4.8-base amd64 4.8-20130123-1 [147 kB] Get:2 http://localhost/debian/ experimental/main libc6-dev amd64 2.16-0experimental1 [3086 kB] Get:3 http://localhost/debian/ experimental/main libc-dev-bin amd64 2.16-0experimental1 [226 kB] Get:4 http://localhost/debian/ experimental/main libc6 amd64 2.16-0experimental1 [4729 kB] Get:5 http://localhost/debian/ experimental/main libgcc1 amd64 1:4.8-20130123-1 [43.7 kB] Get:6 http://localhost/debian/ experimental/main libstdc++6 amd64 4.8-20130123-1 [336 kB] Get:7 http://localhost/debian/ experimental/main libtinfo5 amd64 5.9+20130119-1 [294 kB] Get:8 http://localhost/debian/ experimental/main libncurses5 amd64 5.9+20130119-1 [115 kB] Get:9 http://localhost/debian/ experimental/main libncursesw5 amd64 5.9+20130119-1 [142 kB] Get:10 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-4 [1213 kB] Get:11 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.15.2-1 [463 kB] Get:12 http://localhost/debian/ experimental/main libexpat1 amd64 2.1.0-2 [138 kB] Get:13 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:14 http://localhost/debian/ experimental/main libgomp1 amd64 4.8-20130123-1 [27.4 kB] Get:15 http://localhost/debian/ experimental/main libitm1 amd64 4.8-20130123-1 [37.7 kB] Get:16 http://localhost/debian/ unstable/main libllvm3.2 amd64 3.2-2 [7865 kB] Get:17 http://localhost/debian/ experimental/main libobjc4 amd64 4.8-20130123-1 [163 kB] Get:18 http://localhost/debian/ experimental/main libquadmath0 amd64 4.8-20130123-1 [139 kB] Get:19 http://localhost/debian/ experimental/main libstdc++6-4.7-dev amd64 4.7.2-19 [1678 kB] Get:20 http://localhost/debian/ experimental/main g++-4.7 amd64 4.7.2-19 [5877 kB] Get:21 http://localhost/debian/ experimental/main gcc-4.7 amd64 4.7.2-19 [5831 kB] Get:22 http://localhost/debian/ experimental/main cpp-4.7 amd64 4.7.2-19 [5416 kB] Get:23 http://localhost/debian/ experimental/main libgcc-4.7-dev amd64 4.7.2-19 [2465 kB] Get:24 http://localhost/debian/ experimental/main gcc-4.7-base amd64 4.7.2-19 [148 kB] Get:25 http://localhost/debian/ experimental/main mime-support all 3.53~experimental2 [36.5 kB] Get:26 http://localhost/debian/ experimental/main libpython2.7-minimal amd64 2.7.3-15 [531 kB] Get:27 http://localhost/debian/ experimental/main python2.7-minimal amd64 2.7.3-15 [1220 kB] Get:28 http://localhost/debian/ experimental/main libpython2.7-stdlib amd64 2.7.3-15 [2367 kB] Get:29 http://localhost/debian/ experimental/main python2.7 amd64 2.7.3-15 [326 kB] Get:30 http://localhost/debian/ experimental/main python-minimal amd64 2.7.3-10 [41.8 kB] Get:31 http://localhost/debian/ experimental/main python amd64 2.7.3-10 [184 kB] Get:32 http://localhost/debian/ experimental/main libobjc-4.7-dev amd64 4.7.2-19 [717 kB] Get:33 http://localhost/debian/ experimental/main libclang-common-dev amd64 3.2-1~exp5 [303 kB] Get:34 http://localhost/debian/ experimental/main compiler-rt amd64 3.2-1~exp5 [315 kB] Get:35 http://localhost/debian/ experimental/main clang-3.2 amd64 3.2-1~exp5 [10.1 MB] Get:36 http://localhost/debian/ experimental/main clang all 3.2-1~exp5 [9506 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.7 MB in 1s (33.6 MB/s) Selecting previously unselected package gcc-4.8-base:amd64. (Reading database ... 13484 files and directories currently installed.) Unpacking gcc-4.8-base:amd64 (from .../gcc-4.8-base_4.8-20130123-1_amd64.deb) ... Setting up gcc-4.8-base:amd64 (4.8-20130123-1) ... (Reading database ... 13491 files and directories currently installed.) Preparing to replace libc6-dev:amd64 2.13-38 (using .../libc6-dev_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc6-dev:amd64 ... Preparing to replace libc-dev-bin 2.13-38 (using .../libc-dev-bin_2.16-0experimental1_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6:amd64 2.13-38 (using .../libc6_2.16-0experimental1_amd64.deb) ... 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 Checking for services that may need to be restarted... Checking init scripts... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.16-0experimental1) ... 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 Checking for services that may need to be restarted... Checking init scripts... Nothing to restart. (Reading database ... 13509 files and directories currently installed.) Preparing to replace libgcc1:amd64 1:4.7.2-5 (using .../libgcc1_1%3a4.8-20130123-1_amd64.deb) ... Unpacking replacement libgcc1:amd64 ... Setting up libgcc1:amd64 (1:4.8-20130123-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libstdc++6:amd64 4.7.2-5 (using .../libstdc++6_4.8-20130123-1_amd64.deb) ... Unpacking replacement libstdc++6:amd64 ... Setting up libstdc++6:amd64 (4.8-20130123-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libtinfo5:amd64 5.9-10 (using .../libtinfo5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libtinfo5:amd64 ... Setting up libtinfo5:amd64 (5.9+20130119-1) ... (Reading database ... 13509 files and directories currently installed.) Preparing to replace libncurses5:amd64 5.9-10 (using .../libncurses5_5.9+20130119-1_amd64.deb) ... Unpacking replacement libncurses5:amd64 ... Setting up libncurses5:amd64 (5.9+20130119-1) ... Selecting previously unselected package libncursesw5:amd64. (Reading database ... 13509 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130119-1_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_2.1.0-2_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Preparing to replace libgomp1:amd64 4.7.2-5 (using .../libgomp1_4.8-20130123-1_amd64.deb) ... Unpacking replacement libgomp1:amd64 ... Preparing to replace libitm1:amd64 4.7.2-5 (using .../libitm1_4.8-20130123-1_amd64.deb) ... Unpacking replacement libitm1:amd64 ... Selecting previously unselected package libllvm3.2:amd64. Unpacking libllvm3.2:amd64 (from .../libllvm3.2_3.2-2_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8-20130123-1_amd64.deb) ... Preparing to replace libquadmath0:amd64 4.7.2-5 (using .../libquadmath0_4.8-20130123-1_amd64.deb) ... Unpacking replacement libquadmath0:amd64 ... Preparing to replace libstdc++6-4.7-dev 4.7.2-5 (using .../libstdc++6-4.7-dev_4.7.2-19_amd64.deb) ... Unpacking replacement libstdc++6-4.7-dev:amd64 ... Preparing to replace g++-4.7 4.7.2-5 (using .../g++-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement g++-4.7 ... Preparing to replace gcc-4.7 4.7.2-5 (using .../gcc-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.2-5 (using .../cpp-4.7_4.7.2-19_amd64.deb) ... Unpacking replacement cpp-4.7 ... Selecting previously unselected package libgcc-4.7-dev:amd64. Unpacking libgcc-4.7-dev:amd64 (from .../libgcc-4.7-dev_4.7.2-19_amd64.deb) ... Preparing to replace gcc-4.7-base:amd64 4.7.2-5 (using .../gcc-4.7-base_4.7.2-19_amd64.deb) ... Unpacking replacement gcc-4.7-base:amd64 ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.53~experimental2_all.deb) ... Selecting previously unselected package libpython2.7-minimal:amd64. Unpacking libpython2.7-minimal:amd64 (from .../libpython2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-15_amd64.deb) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Unpacking libpython2.7-stdlib:amd64 (from .../libpython2.7-stdlib_2.7.3-15_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-15_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3-10_amd64.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-10_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.2-19_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package compiler-rt. Unpacking compiler-rt (from .../compiler-rt_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang-3.2. Unpacking clang-3.2 (from .../clang-3.2_3.2-1~exp5_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../clang_3.2-1~exp5_all.deb) ... Setting up libc-dev-bin (2.16-0experimental1) ... Setting up libc6-dev:amd64 (2.16-0experimental1) ... Setting up libncursesw5:amd64 (5.9+20130119-1) ... 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 (2.1.0-2) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libgomp1:amd64 (4.8-20130123-1) ... Setting up libitm1:amd64 (4.8-20130123-1) ... Setting up libllvm3.2:amd64 (3.2-2) ... Setting up libobjc4:amd64 (4.8-20130123-1) ... Setting up libquadmath0:amd64 (4.8-20130123-1) ... Setting up gcc-4.7-base:amd64 (4.7.2-19) ... Setting up libgcc-4.7-dev:amd64 (4.7.2-19) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.2-19) ... Setting up cpp-4.7 (4.7.2-19) ... Setting up gcc-4.7 (4.7.2-19) ... Setting up g++-4.7 (4.7.2-19) ... Setting up mime-support (3.53~experimental2) ... Setting up libpython2.7-minimal:amd64 (2.7.3-15) ... Setting up python2.7-minimal (2.7.3-15) ... Linking and byte-compiling packages for runtime python2.7... Setting up libpython2.7-stdlib:amd64 (2.7.3-15) ... Setting up python2.7 (2.7.3-15) ... Setting up python-minimal (2.7.3-10) ... Setting up python (2.7.3-10) ... Setting up libobjc-4.7-dev:amd64 (4.7.2-19) ... Setting up libclang-common-dev (3.2-1~exp5) ... Setting up compiler-rt (3.2-1~exp5) ... Setting up clang-3.2 (3.2-1~exp5) ... Setting up clang (3.2-1~exp5) ... + 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 - /build/ncbi-blast+-2ZgS7v + 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 `/build/ncbi-blast+-2ZgS7v/resolver-PzQz5p/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 ... 14674 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), autotools-dev (>= 20100122), debhelper (>= 7.0.50~), dpkg-dev (>= 1.16.1), libboost-test-dev, libbz2-dev, libpcre3-dev, quilt (>= 0.46-7~), time, zlib1g-dev 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), autotools-dev (>= 20100122), debhelper (>= 7.0.50~), dpkg-dev (>= 1.16.1), libboost-test-dev, libbz2-dev, libpcre3-dev, quilt (>= 0.46-7~), time, zlib1g-dev dpkg-deb: building package `sbuild-build-depends-ncbi-blast+-dummy' in `/build/ncbi-blast+-2ZgS7v/resolver-ySm56c/apt_archive/sbuild-build-depends-ncbi-blast+-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install ncbi-blast+ build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libasprintf-dev libasprintf0c2 libboost-test-dev libboost-test1.49-dev libboost-test1.49.0 libboost1.49-dev libbz2-dev libcroco3 libgettextpo-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt time zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost1.49-doc libboost-chrono1.49-dev libboost-date-time1.49-dev libboost-filesystem1.49-dev libboost-graph-parallel1.49-dev libboost-graph1.49-dev libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev libboost-mpi1.49-dev libboost-program-options1.49-dev libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev libboost-serialization1.49-dev libboost-signals1.49-dev libboost-system1.49-dev libboost-thread1.49-dev libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libasprintf-dev libasprintf0c2 libboost-test-dev libboost-test1.49-dev libboost-test1.49.0 libboost1.49-dev libbz2-dev libcroco3 libgettextpo-dev libgettextpo0 libglib2.0-0 libicu48 libmagic1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-ncbi-blast+-dummy time zlib1g-dev 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB/25.4 MB of archives. After this operation, 149 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 libicu48 amd64 4.8.1.1-10 [4741 kB] Get:14 http://localhost/debian/ unstable/main libpcrecpp0 amd64 1:8.31-2 [128 kB] Get:15 http://localhost/debian/ unstable/main file amd64 5.11-2 [51.8 kB] Get:16 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-10 [154 kB] Get:17 http://localhost/debian/ unstable/main time amd64 1.7-24 [34.1 kB] Get:18 http://localhost/debian/ unstable/main autotools-dev all 20120608.1 [73.0 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 diffstat amd64 1.55-3 [30.0 kB] Get:27 http://localhost/debian/ unstable/main libboost1.49-dev amd64 1.49.0-3.1 [9203 kB] Get:28 http://localhost/debian/ unstable/main libboost-test1.49.0 amd64 1.49.0-3.1 [294 kB] Get:29 http://localhost/debian/ unstable/main libboost-test1.49-dev amd64 1.49.0-3.1 [756 kB] Get:30 http://localhost/debian/ unstable/main libboost-test-dev amd64 1.49.0.1 [2750 B] Get:31 http://localhost/debian/ unstable/main libbz2-dev amd64 1.0.6-4 [32.8 kB] Get:32 http://localhost/debian/ unstable/main libpcre3-dev amd64 1:8.31-2 [356 kB] Get:33 http://localhost/debian/ unstable/main quilt all 0.60-7 [381 kB] Get:34 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.4 MB in 0s (25.4 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14674 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. 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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 libicu48:amd64 (4.8.1.1-10) ... Setting up libpcrecpp0:amd64 (1:8.31-2) ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-10) ... Setting up time (1.7-24) ... Setting up autotools-dev (20120608.1) ... Setting up html2text (1.3.2a-15) ... 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Setting up sbuild-build-depends-ncbi-blast+-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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_4.7.2-19 gcc-4.6_4.6.3-15 gcc-4.7_4.7.2-19 libc6-dev_2.16-0experimental1 libstdc++6_4.8-20130123-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 linux-libc-dev_3.2.35-2 Package versions: apt_0.9.7.7 autotools-dev_20120608.1 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_3.2-1~exp5 clang-3.2_3.2-1~exp5 compiler-rt_3.2-1~exp5 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.6_4.6.3-15 cpp-4.7_4.7.2-19 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 diffstat_1.55-3 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_4.7.2-19 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_4.7.2-19 gcc-4.7-base_4.7.2-19 gcc-4.8-base_4.8-20130123-1 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 libblkid1_2.20.1-5.3 libboost-test-dev_1.49.0.1 libboost-test1.49-dev_1.49.0-3.1 libboost-test1.49.0_1.49.0-3.1 libboost1.49-dev_1.49.0-3.1 libbz2-1.0_1.0.6-4 libbz2-dev_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.16-0experimental1 libc6_2.16-0experimental1 libc6-dev_2.16-0experimental1 libclang-common-dev_3.2-1~exp5 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_2.1.0-2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc-4.7-dev_4.7.2-19 libgcc1_1:4.8-20130123-1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.8-20130123-1 libgpm2_1.20.4-6 libicu48_4.8.1.1-10 libitm1_4.8-20130123-1 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+20130119-1 libncursesw5_5.9+20130119-1 libobjc-4.7-dev_4.7.2-19 libobjc4_4.8-20130123-1 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 libpcre3-dev_1:8.31-2 libpcrecpp0_1:8.31-2 libpipeline1_1.2.2-1 libpython2.7-minimal_2.7.3-15 libpython2.7-stdlib_2.7.3-15 libquadmath0_4.8-20130123-1 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 libssl1.0.0_1.0.1c-4 libstdc++6_4.8-20130123-1 libstdc++6-4.6-dev_4.6.3-15 libstdc++6-4.7-dev_4.7.2-19 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+20130119-1 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_3.53~experimental2 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_2.7.3-10 python-minimal_2.7.3-10 python2.7_2.7.3-15 python2.7-minimal_2.7.3-15 quilt_0.60-7 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ncbi-blast+-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 time_1.7-24 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 Oct 5 14:12:22 2012 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./ncbi-blast+_2.2.27-3.dsc dpkg-source: info: extracting ncbi-blast+ in ncbi-blast+-2.2.27 dpkg-source: info: unpacking ncbi-blast+_2.2.27.orig.tar.gz dpkg-source: info: unpacking ncbi-blast+_2.2.27-3.debian.tar.gz dpkg-source: info: applying hurd_fixes dpkg-source: info: applying legacy_rename_rpsblast dpkg-source: info: applying fix_lib_deps dpkg-source: info: applying no_multiarch_rpath dpkg-source: info: applying use_pie_for_apps dpkg-source: info: applying fix_arm_mips_build 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-248a94f5-6bfd-469d-8e2e-d938670141e9 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package ncbi-blast+ dpkg-buildpackage: source version 2.2.27-3 dpkg-buildpackage: source changed by Olivier Sallou dpkg-source --before-build ncbi-blast+-2.2.27 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean -Dc++ --with autotools_dev --with quilt dh_testdir -O-Dc\+\+ dh_auto_clean -O-Dc\+\+ dh_autotools-dev_restoreconfig -O-Dc\+\+ dh_quilt_unpatch -O-Dc\+\+ Removing patch fix_arm_mips_build Restoring c++/include/corelib/ncbitype.h Removing patch use_pie_for_apps Restoring c++/src/build-system/Makefile.app.in Removing patch no_multiarch_rpath Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure Removing patch fix_lib_deps Restoring c++/src/serial/Makefile.serial.lib Restoring c++/src/corelib/Makefile.test_mt.lib Restoring c++/src/corelib/Makefile.test_boost.lib Restoring c++/src/util/xregexp/Makefile.xregexp.lib Restoring c++/src/util/Makefile.util.lib Restoring c++/src/util/sequtil/Makefile.sequtil.lib Restoring c++/src/util/compress/api/Makefile.compress.lib Restoring c++/src/objmgr/split/Makefile.id2_split.lib Restoring c++/src/objmgr/util/Makefile.util.lib Restoring c++/src/connect/ext/Makefile.xconnext.lib Restoring c++/src/connect/Makefile.xconnect.lib Restoring c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib Restoring c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib Restoring c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib Restoring c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib Restoring c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib Restoring c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib Restoring c++/src/objtools/blast/services/Makefile.blast_services.lib Restoring c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib Restoring c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib Restoring c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib Restoring c++/src/objtools/simple/Makefile.xobjsimple.lib Restoring c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib Restoring c++/src/objtools/readers/Makefile.xobjread.lib Restoring c++/src/objtools/alnmgr/Makefile.alnmgr.lib Restoring c++/src/objtools/align_format/Makefile.align_format.lib Restoring c++/src/objects/seqsplit/Makefile.seqsplit.lib Restoring c++/src/objects/seqset/Makefile.seqset.lib Restoring c++/src/objects/seqcode/Makefile.seqcode.lib Restoring c++/src/objects/seq/Makefile.seq.lib Restoring c++/src/objects/pub/Makefile.pub.lib Restoring c++/src/objects/medline/Makefile.medline.lib Restoring c++/src/objects/id2/Makefile.id2.lib Restoring c++/src/objects/id1/Makefile.id1.lib Restoring c++/src/objects/genomecoll/Makefile.genome_collection.lib Restoring c++/src/objects/general/Makefile.general.lib Restoring c++/src/objects/blastdb/Makefile.blastdb.lib Restoring c++/src/objects/biblio/Makefile.biblio.lib Restoring c++/src/objects/submit/Makefile.submit.lib Restoring c++/src/objects/seqedit/Makefile.seqedit.lib Restoring c++/src/objects/scoremat/Makefile.scoremat.lib Restoring c++/src/objects/entrez2/Makefile.entrez2cli.lib Restoring c++/src/objects/entrez2/Makefile.entrez2.lib Restoring c++/src/objects/blastxml/Makefile.blastxml.lib Restoring c++/src/objects/blast/Makefile.blast.lib Restoring c++/src/objects/blast/Makefile.xnetblastcli.lib Restoring c++/src/html/Makefile.html.lib Restoring c++/src/cgi/Makefile.cgi.lib Restoring c++/src/algo/segmask/Makefile.xalgosegmask.lib Restoring c++/src/algo/dustmask/Makefile.xalgodustmask.lib Restoring c++/src/algo/winmask/Makefile.xalgowinmask.lib Restoring c++/src/algo/blast/Makefile.blast_macros.mk Restoring c++/src/algo/blast/blastinput/Makefile.blastinput.lib Restoring c++/src/algo/blast/api/Makefile.xblast.lib Restoring c++/src/algo/blast/format/Makefile.xblastformat.lib Restoring c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app Restoring c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib Restoring c++/src/algo/blast/core/Makefile.blast.lib Removing patch legacy_rename_rpsblast Restoring c++/src/app/blast/legacy_blast.pl Removing patch hurd_fixes Restoring c++/src/connect/ext/ncbi_localnet.c Restoring c++/src/connect/ncbi_socket_cxx.cpp Restoring c++/src/build-system/configure.ac Restoring c++/src/build-system/configure No patches applied debian/rules override_dh_clean make[1]: Entering directory `/build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27' dh_clean for x in c++/src/objects/*/*.files; do \ if [ -d $x ]; then \ (cd `dirname $x` && ../../../BUILD/build/new_module.sh \ `basename $x .files`.module purge_sources); \ fi \ done rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module make[1]: Leaving directory `/build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27' debian/rules build-arch dh build-arch -Dc++ --with autotools_dev --with quilt dh_testdir -a -O-Dc\+\+ dh_autotools-dev_updateconfig -a -O-Dc\+\+ dh_quilt_patch -a -O-Dc\+\+ Applying patch hurd_fixes patching file c++/src/build-system/configure patching file c++/src/build-system/configure.ac patching file c++/src/connect/ncbi_socket_cxx.cpp patching file c++/src/connect/ext/ncbi_localnet.c Applying patch legacy_rename_rpsblast patching file c++/src/app/blast/legacy_blast.pl Applying patch fix_lib_deps patching file c++/src/algo/blast/core/Makefile.blast.lib patching file c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib patching file c++/src/algo/blast/format/Makefile.xblastformat.lib patching file c++/src/algo/winmask/Makefile.xalgowinmask.lib patching file c++/src/cgi/Makefile.cgi.lib patching file c++/src/html/Makefile.html.lib patching file c++/src/objects/blast/Makefile.xnetblastcli.lib patching file c++/src/objtools/align_format/Makefile.align_format.lib patching file c++/src/objtools/alnmgr/Makefile.alnmgr.lib patching file c++/src/objtools/readers/Makefile.xobjread.lib patching file c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib patching file c++/src/objtools/simple/Makefile.xobjsimple.lib patching file c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib patching file c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib patching file c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib patching file c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib patching file c++/src/algo/blast/api/Makefile.xblast.lib patching file c++/src/algo/blast/blastinput/Makefile.blastinput.lib patching file c++/src/algo/dustmask/Makefile.xalgodustmask.lib patching file c++/src/connect/Makefile.xconnect.lib patching file c++/src/connect/ext/Makefile.xconnext.lib patching file c++/src/objects/blast/Makefile.blast.lib patching file c++/src/objects/blastxml/Makefile.blastxml.lib patching file c++/src/objects/entrez2/Makefile.entrez2.lib patching file c++/src/objects/entrez2/Makefile.entrez2cli.lib patching file c++/src/objects/scoremat/Makefile.scoremat.lib patching file c++/src/objects/seqedit/Makefile.seqedit.lib patching file c++/src/objects/submit/Makefile.submit.lib patching file c++/src/objmgr/util/Makefile.util.lib patching file c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib patching file c++/src/objtools/blast/services/Makefile.blast_services.lib patching file c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib patching file c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib patching file c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib patching file c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib patching file c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib patching file c++/src/util/compress/api/Makefile.compress.lib patching file c++/src/util/sequtil/Makefile.sequtil.lib patching file c++/src/corelib/Makefile.test_boost.lib patching file c++/src/corelib/Makefile.test_mt.lib patching file c++/src/objects/biblio/Makefile.biblio.lib patching file c++/src/objects/blastdb/Makefile.blastdb.lib patching file c++/src/objects/general/Makefile.general.lib patching file c++/src/objects/genomecoll/Makefile.genome_collection.lib patching file c++/src/objects/id1/Makefile.id1.lib patching file c++/src/objects/id2/Makefile.id2.lib patching file c++/src/objects/medline/Makefile.medline.lib patching file c++/src/objects/pub/Makefile.pub.lib patching file c++/src/objects/seq/Makefile.seq.lib patching file c++/src/objects/seqcode/Makefile.seqcode.lib patching file c++/src/objects/seqset/Makefile.seqset.lib patching file c++/src/objects/seqsplit/Makefile.seqsplit.lib patching file c++/src/serial/Makefile.serial.lib patching file c++/src/util/Makefile.util.lib patching file c++/src/util/xregexp/Makefile.xregexp.lib patching file c++/src/algo/segmask/Makefile.xalgosegmask.lib patching file c++/src/objmgr/split/Makefile.id2_split.lib patching file c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib patching file c++/src/algo/blast/Makefile.blast_macros.mk patching file c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app Applying patch no_multiarch_rpath patching file c++/src/build-system/configure patching file c++/src/build-system/configure.ac Applying patch use_pie_for_apps patching file c++/src/build-system/Makefile.app.in Applying patch fix_arm_mips_build patching file c++/include/corelib/ncbitype.h Now at patch fix_arm_mips_build debian/rules override_dh_auto_configure make[1]: Entering directory `/build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27' cd c++ && LD_LIBRARY_PATH=/build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27/c++/BUILD/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH} \ CONFIG_SHELL=/bin/bash ./configure --with-dll --with-mt --without-autodep --without-makefile-auto-update --with-flat-makefile --without-caution --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD --without-debug configure: loading site script ./src/build-system/config.site configure: creating cache config.cache checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes adjusted C compiler: /usr/bin/gcc adjusted C++ compiler: /usr/bin/g++ checking whether /usr/bin/gcc supports -Wl,-E... yes checking whether /usr/bin/gcc supports -Wl,--{en,dis}able-new-dtags... yes checking whether ln -s works... yes checking for ranlib... ranlib checking for ar... ar cr checking ranlib's effectiveness... neutral checking for ccache... no checking for tail... /usr/bin/tail checking whether /usr/bin/tail accepts modern syntax (-n N)... yes checking for touch... /bin/touch checking for egrep... grep -E checking how to run grep -E quietly... grep -E -q checking for valgrind... no checking how to run the C++ preprocessor... /usr/bin/g++ -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... no checking for string.h... no checking for memory.h... no checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... no checking for size_t... yes checking for size_t... (cached) yes configure: error: cannot compute sizeof (size_t), 77 See `config.log' for more details. make[1]: *** [override_dh_auto_configure] Error 1 checking size of size_t... make[1]: Leaving directory `/build/ncbi-blast+-2ZgS7v/ncbi-blast+-2.2.27' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130128-0408 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /build/ncbi-blast+-2ZgS7v Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 89628 Build-Time: 8 Distribution: unstable Fail-Stage: build Install-Time: 11 Job: ncbi-blast+_2.2.27-3 Package: ncbi-blast+ Package-Time: 50 Source-Version: 2.2.27-3 Space: 89628 Status: attempted Version: 2.2.27-3 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130128-0408 Build needed 00:00:50, 89628k disc space DC-Status: Failed 50.993385s DC-Time-Estimation: 50.993385 versus expected 10762 (r/m: 210.04698187814 ; m: 50.993385)