RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux beebe 3.8.0-mustang_sw_1.08.12-beta_rc #1 SMP Fri Oct 18 15:13:20 PDT 2013 aarch64 Buildd toolchain package versions: launchpad-buildd_119~APM.12.04.2 python-lpbuildd_119~APM.12.04.2. Syncing the system clock with the buildd NTP service... 15 Dec 07:45:38 ntpdate[22097]: adjust time server 10.211.37.1 offset -0.051890 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5337386', '/home/buildd/filecache-default/a24bd41060605d4f5aef5746aacf39703b0275a9'] Unpacking chroot for build PACKAGEBUILD-5337386 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5337386'] Mounting chroot for build PACKAGEBUILD-5337386 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5337386', 'deb http://ftpmaster.internal/ubuntu trusty main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-5337386 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5337386', 'arm64'] Updating debian chroot for build PACKAGEBUILD-5337386 Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty-updates InRelease Hit http://archive-team.internal trusty Release Ign http://ftpmaster.internal trusty-proposed InRelease Ign http://archive-team.internal trusty/main arm64 Packages/DiffIndex Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Get:2 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:4 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty Release [58.5 kB] Ign http://archive-team.internal trusty/main Translation-en Hit http://archive-team.internal trusty/main arm64 Packages Get:6 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:7 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:8 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:9 http://ftpmaster.internal trusty/main arm64 Packages [1168 kB] Get:10 http://ftpmaster.internal trusty/restricted arm64 Packages [14 B] Get:11 http://ftpmaster.internal trusty/universe arm64 Packages [4847 kB] Get:12 http://ftpmaster.internal trusty/multiverse arm64 Packages [103 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [729 kB] Get:14 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:15 http://ftpmaster.internal trusty/restricted Translation-en [3433 B] Get:16 http://ftpmaster.internal trusty/universe Translation-en [3999 kB] Get:17 http://ftpmaster.internal trusty-security/main arm64 Packages [14 B] Get:18 http://ftpmaster.internal trusty-security/restricted arm64 Packages [14 B] Get:19 http://ftpmaster.internal trusty-security/universe arm64 Packages [14 B] Get:20 http://ftpmaster.internal trusty-security/multiverse arm64 Packages [14 B] Get:21 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:22 http://ftpmaster.internal trusty-security/multiverse Translation-en [14 B] Get:23 http://ftpmaster.internal trusty-security/restricted Translation-en [14 B] Get:24 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:25 http://ftpmaster.internal trusty-updates/main arm64 Packages [14 B] Get:26 http://ftpmaster.internal trusty-updates/restricted arm64 Packages [14 B] Get:27 http://ftpmaster.internal trusty-updates/universe arm64 Packages [14 B] Get:28 http://ftpmaster.internal trusty-updates/multiverse arm64 Packages [14 B] Get:29 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:30 http://ftpmaster.internal trusty-updates/multiverse Translation-en [14 B] Get:31 http://ftpmaster.internal trusty-updates/restricted Translation-en [14 B] Get:32 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:33 http://ftpmaster.internal trusty-proposed/main arm64 Packages [11.2 kB] Get:34 http://ftpmaster.internal trusty-proposed/restricted arm64 Packages [14 B] Get:35 http://ftpmaster.internal trusty-proposed/universe arm64 Packages [138 kB] Get:36 http://ftpmaster.internal trusty-proposed/multiverse arm64 Packages [2904 B] Get:37 http://ftpmaster.internal trusty-proposed/main Translation-en [13.7 kB] Get:38 http://ftpmaster.internal trusty-proposed/multiverse Translation-en [3953 B] Get:39 http://ftpmaster.internal trusty-proposed/restricted Translation-en [14 B] Get:40 http://ftpmaster.internal trusty-proposed/universe Translation-en [134 kB] Fetched 11.5 MB in 11s (1018 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https binutils build-essential cpp cpp-4.8 e2fslibs e2fsprogs fakeroot g++ g++-4.8 gcc gcc-4.8 gcc-4.8-base hostname libapt-pkg4.12 libatomic1 libcomerr2 libfakeroot libgcc-4.8-dev libgcc1 libgcrypt11 libgomp1 liblockfile-bin liblockfile1 libplymouth2 libsqlite3-0 libss2 libstdc++-4.8-dev libstdc++6 linux-libc-dev perl perl-base perl-modules plymouth sed tar 37 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After this operation, 1810 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs arm64 1.42.8-1ubuntu3 [158 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs arm64 1.42.8-1ubuntu3 [616 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main hostname arm64 3.15ubuntu1 [11.0 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-proposed/main perl arm64 5.18.1-5 [2211 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty-proposed/main perl-base arm64 5.18.1-5 [1010 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-proposed/main perl-modules all 5.18.1-5 [2680 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main sed arm64 4.2.2-2ubuntu2 [134 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main tar arm64 1.27-4 [169 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 arm64 4.8.2-10ubuntu1 [19.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base arm64 4.8.2-10ubuntu1 [14.8 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 arm64 1:4.8.2-10ubuntu1 [29.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 arm64 4.8.2-10ubuntu1 [6088 B] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 arm64 4.8.2-10ubuntu1 [3526 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev arm64 4.8.2-10ubuntu1 [1050 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 arm64 4.8.2-10ubuntu1 [5344 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 arm64 4.8.2-10ubuntu1 [3924 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev arm64 4.8.2-10ubuntu1 [131 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 arm64 4.8.2-10ubuntu1 [210 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main binutils arm64 2.24-2ubuntu1 [1028 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libapt-pkg4.12 arm64 0.9.14.1ubuntu1 [574 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main apt arm64 0.9.14.1ubuntu1 [942 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 arm64 1.42.8-1ubuntu3 [60.5 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libss2 arm64 1.42.8-1ubuntu3 [64.0 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgcrypt11 arm64 1.5.3-2ubuntu2 [217 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main liblockfile-bin arm64 1.09-6ubuntu1 [10.2 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main liblockfile1 arm64 1.09-6ubuntu1 [7158 B] Get:27 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libsqlite3-0 arm64 3.8.1-1ubuntu3 [278 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main plymouth arm64 0.8.8-0ubuntu12 [81.7 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main libplymouth2 arm64 0.8.8-0ubuntu12 [61.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main apt-transport-https arm64 0.9.14.1ubuntu1 [24.4 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main cpp arm64 4:4.8.2-1ubuntu2 [27.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main gcc arm64 4:4.8.2-1ubuntu2 [4998 B] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main g++ arm64 4:4.8.2-1ubuntu2 [1482 B] Get:34 http://ftpmaster.internal/ubuntu/ trusty-proposed/main build-essential arm64 11.6ubuntu6 [4828 B] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main libfakeroot arm64 1.20-3ubuntu1 [20.6 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main fakeroot arm64 1.20-3ubuntu1 [52.8 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main linux-libc-dev arm64 3.12.0-7.15 [702 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.4 MB in 17s (1457 kB/s) (Reading database ... 11898 files and directories currently installed.) Preparing to replace e2fslibs:arm64 1.42.8-1ubuntu1 (using .../e2fslibs_1.42.8-1ubuntu3_arm64.deb) ... Unpacking replacement e2fslibs:arm64 ... Setting up e2fslibs:arm64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace e2fsprogs 1.42.8-1ubuntu1 (using .../e2fsprogs_1.42.8-1ubuntu3_arm64.deb) ... Unpacking replacement e2fsprogs ... Setting up e2fsprogs (1.42.8-1ubuntu3) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace hostname 3.13ubuntu1 (using .../hostname_3.15ubuntu1_arm64.deb) ... Unpacking replacement hostname ... Setting up hostname (3.15ubuntu1) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace perl 5.18.1-4build1 (using .../perl_5.18.1-5_arm64.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.18.1-4build1 (using .../perl-base_5.18.1-5_arm64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.18.1-5) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace perl-modules 5.18.1-4build1 (using .../perl-modules_5.18.1-5_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace sed 4.2.2-2ubuntu1 (using .../sed_4.2.2-2ubuntu2_arm64.deb) ... Unpacking replacement sed ... Setting up sed (4.2.2-2ubuntu2) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace tar 1.27-3 (using .../archives/tar_1.27-4_arm64.deb) ... Unpacking replacement tar ... Setting up tar (1.27-4) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace libgomp1:arm64 4.8.2-1ubuntu2 (using .../libgomp1_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libgomp1:arm64 ... Preparing to replace gcc-4.8-base:arm64 4.8.2-1ubuntu2 (using .../gcc-4.8-base_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement gcc-4.8-base:arm64 ... Setting up gcc-4.8-base:arm64 (4.8.2-10ubuntu1) ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace libgcc1:arm64 1:4.8.2-1ubuntu2 (using .../libgcc1_1%3a4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libgcc1:arm64 ... Setting up libgcc1:arm64 (1:4.8.2-10ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11898 files and directories currently installed.) Preparing to replace libatomic1:arm64 4.8.2-1ubuntu2 (using .../libatomic1_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libatomic1:arm64 ... Preparing to replace cpp-4.8 4.8.2-1ubuntu2 (using .../cpp-4.8_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement cpp-4.8 ... Preparing to replace libstdc++-4.8-dev:arm64 4.8.2-1ubuntu2 (using .../libstdc++-4.8-dev_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libstdc++-4.8-dev:arm64 ... Preparing to replace g++-4.8 4.8.2-1ubuntu2 (using .../g++-4.8_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement g++-4.8 ... Preparing to replace gcc-4.8 4.8.2-1ubuntu2 (using .../gcc-4.8_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement gcc-4.8 ... Preparing to replace libgcc-4.8-dev:arm64 4.8.2-1ubuntu2 (using .../libgcc-4.8-dev_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libgcc-4.8-dev:arm64 ... Preparing to replace libstdc++6:arm64 4.8.2-1ubuntu2 (using .../libstdc++6_4.8.2-10ubuntu1_arm64.deb) ... Unpacking replacement libstdc++6:arm64 ... Setting up libstdc++6:arm64 (4.8.2-10ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11914 files and directories currently installed.) Preparing to replace binutils 2.24-1ubuntu2 (using .../binutils_2.24-2ubuntu1_arm64.deb) ... Unpacking replacement binutils ... Preparing to replace libapt-pkg4.12:arm64 0.9.13.1~ubuntu1 (using .../libapt-pkg4.12_0.9.14.1ubuntu1_arm64.deb) ... Unpacking replacement libapt-pkg4.12:arm64 ... Setting up libapt-pkg4.12:arm64 (0.9.14.1ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11914 files and directories currently installed.) Preparing to replace apt 0.9.13.1~ubuntu1 (using .../apt_0.9.14.1ubuntu1_arm64.deb) ... Unpacking replacement apt ... Setting up apt (0.9.14.1ubuntu1) ... (Reading database ... 11914 files and directories currently installed.) Preparing to replace libcomerr2:arm64 1.42.8-1ubuntu1 (using .../libcomerr2_1.42.8-1ubuntu3_arm64.deb) ... Unpacking replacement libcomerr2:arm64 ... Setting up libcomerr2:arm64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11914 files and directories currently installed.) Preparing to replace libss2:arm64 1.42.8-1ubuntu1 (using .../libss2_1.42.8-1ubuntu3_arm64.deb) ... Unpacking replacement libss2:arm64 ... Setting up libss2:arm64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11914 files and directories currently installed.) Preparing to replace libgcrypt11:arm64 1.5.3-2ubuntu1 (using .../libgcrypt11_1.5.3-2ubuntu2_arm64.deb) ... Unpacking replacement libgcrypt11:arm64 ... Preparing to replace liblockfile-bin 1.09-6 (using .../liblockfile-bin_1.09-6ubuntu1_arm64.deb) ... Unpacking replacement liblockfile-bin ... Preparing to replace liblockfile1:arm64 1.09-6 (using .../liblockfile1_1.09-6ubuntu1_arm64.deb) ... Unpacking replacement liblockfile1:arm64 ... Preparing to replace libsqlite3-0:arm64 3.8.1-1ubuntu1 (using .../libsqlite3-0_3.8.1-1ubuntu3_arm64.deb) ... Unpacking replacement libsqlite3-0:arm64 ... Preparing to replace plymouth 0.8.8-0ubuntu11 (using .../plymouth_0.8.8-0ubuntu12_arm64.deb) ... Unpacking replacement plymouth ... Preparing to replace libplymouth2:arm64 0.8.8-0ubuntu11 (using .../libplymouth2_0.8.8-0ubuntu12_arm64.deb) ... Unpacking replacement libplymouth2:arm64 ... Preparing to replace apt-transport-https 0.9.13.1~ubuntu1 (using .../apt-transport-https_0.9.14.1ubuntu1_arm64.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace cpp 4:4.8.1-2ubuntu3 (using .../cpp_4%3a4.8.2-1ubuntu2_arm64.deb) ... Unpacking replacement cpp ... Preparing to replace gcc 4:4.8.1-2ubuntu3 (using .../gcc_4%3a4.8.2-1ubuntu2_arm64.deb) ... Removing old gcc doc directory. Unpacking replacement gcc ... Preparing to replace g++ 4:4.8.1-2ubuntu3 (using .../g++_4%3a4.8.2-1ubuntu2_arm64.deb) ... Unpacking replacement g++ ... Preparing to replace build-essential 11.6ubuntu5 (using .../build-essential_11.6ubuntu6_arm64.deb) ... Unpacking replacement build-essential ... Preparing to replace libfakeroot:arm64 1.20-3 (using .../libfakeroot_1.20-3ubuntu1_arm64.deb) ... Unpacking replacement libfakeroot:arm64 ... Preparing to replace fakeroot 1.20-3 (using .../fakeroot_1.20-3ubuntu1_arm64.deb) ... Unpacking replacement fakeroot ... Preparing to replace linux-libc-dev:arm64 3.12.0-5.13 (using .../linux-libc-dev_3.12.0-7.15_arm64.deb) ... Unpacking replacement linux-libc-dev:arm64 ... Setting up libgomp1:arm64 (4.8.2-10ubuntu1) ... Setting up libatomic1:arm64 (4.8.2-10ubuntu1) ... Setting up cpp-4.8 (4.8.2-10ubuntu1) ... Setting up libgcc-4.8-dev:arm64 (4.8.2-10ubuntu1) ... Setting up libstdc++-4.8-dev:arm64 (4.8.2-10ubuntu1) ... Setting up binutils (2.24-2ubuntu1) ... Setting up gcc-4.8 (4.8.2-10ubuntu1) ... Setting up g++-4.8 (4.8.2-10ubuntu1) ... Setting up libgcrypt11:arm64 (1.5.3-2ubuntu2) ... Setting up liblockfile-bin (1.09-6ubuntu1) ... Setting up liblockfile1:arm64 (1.09-6ubuntu1) ... Setting up libsqlite3-0:arm64 (3.8.1-1ubuntu3) ... Setting up libplymouth2:arm64 (0.8.8-0ubuntu12) ... Setting up plymouth (0.8.8-0ubuntu12) ... update-initramfs: deferring update (trigger activated) Setting up apt-transport-https (0.9.14.1ubuntu1) ... Setting up cpp (4:4.8.2-1ubuntu2) ... Setting up gcc (4:4.8.2-1ubuntu2) ... Setting up g++ (4:4.8.2-1ubuntu2) ... Setting up build-essential (11.6ubuntu6) ... Setting up libfakeroot:arm64 (1.20-3ubuntu1) ... Setting up fakeroot (1.20-3ubuntu1) ... Setting up linux-libc-dev:arm64 (3.12.0-7.15) ... Setting up perl-modules (5.18.1-5) ... Setting up perl (5.18.1-5) ... Processing triggers for libc-bin ... Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5337386', 'arm64', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '--purpose=PRIMARY', '--architecture=arm64', '--comp=multiverse', 'clustalw-mpi_0.15-3build1.dsc'] Initiating build PACKAGEBUILD-5337386 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.8.0-mustang_sw_1.08.12-beta_rc #1 SMP Fri Oct 18 15:13:20 PDT 2013 aarch64 Automatic build of clustalw-mpi_0.15-3build1 on beebe by sbuild/arm64 1.170.5 Build started at 20131215-0747 ****************************************************************************** clustalw-mpi_0.15-3build1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), mpi-default-dev Checking for already installed source dependencies... debhelper: missing mpi-default-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper mpi-default-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base gfortran gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libmagic1 libmpich-dev libmpich10 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc gfortran-doc gfortran-4.8-doc libgfortran3-dbg groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info mpich xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base gfortran gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libmagic1 libmpich-dev libmpich10 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support mpi-default-dev po-debconf python3 python3-minimal python3.3 python3.3-minimal 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 15.4 MB of archives. After this operation, 67.0 MB of additional disk space will be used. 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Setting up libmagic1:arm64 (1:5.14-2ubuntu1) ... Setting up libssl1.0.0:arm64 (1.0.1e-4ubuntu3) ... Setting up libpython3.3-minimal:arm64 (3.3.3-4) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.3-stdlib:arm64 (3.3.3-4) ... Setting up python3.3-minimal (3.3.3-4) ... Setting up libasprintf0c2:arm64 (0.18.3.1-1ubuntu1) ... Setting up libglib2.0-0:arm64 (2.39.1-0ubuntu3) ... No schema files found: doing nothing. Setting up libpipeline1:arm64 (1.2.5-1) ... Setting up libxml2:arm64 (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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'. 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Setting up python3 (3.3.2-17) ... running python rtupdate hooks for python3.3... running python post-rtupdate hooks for python3.3... Setting up dh-python (1.20131021-1ubuntu3) ... Setting up apparmor-easyprof (2.8.0-0ubuntu35) ... Setting up dh-apparmor (2.8.0-0ubuntu35) ... Setting up debhelper (9.20131127ubuntu1) ... Processing triggers for libc-bin ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.17-93ubuntu4 make_3.81-8.2ubuntu3 dpkg-dev_1.17.1ubuntu1 gcc-4.8_4.8.2-10ubuntu1 g++-4.8_4.8.2-10ubuntu1 binutils_2.24-2ubuntu1 libstdc++-4.8-dev_4.8.2-10ubuntu1 libstdc++6_4.8.2-10ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Sun Dec 15 06:04:40 2013 UTC using RSA key ID EA330543 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clustalw-mpi_0.15-3build1.dsc dpkg-source: info: extracting clustalw-mpi in clustalw-mpi-0.15 dpkg-source: info: unpacking clustalw-mpi_0.15.orig.tar.gz dpkg-source: info: unpacking clustalw-mpi_0.15-3build1.debian.tar.gz dpkg-buildpackage: source package clustalw-mpi dpkg-buildpackage: source version 0.15-3build1 dpkg-buildpackage: source distribution trusty dpkg-source --before-build clustalw-mpi-0.15 dpkg-buildpackage: host architecture arm64 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/build/buildd/clustalw-mpi-0.15' /bin/rm -f *.o make[1]: Leaving directory `/build/buildd/clustalw-mpi-0.15' debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/clustalw-mpi-0.15' dh_clean rm -rf clustalw-mpi make[1]: Leaving directory `/build/buildd/clustalw-mpi-0.15' debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make[1]: Entering directory `/build/buildd/clustalw-mpi-0.15' mpicc -c -g clustalw-mpi.c mpicc -c -g interface.c interface.c: In function 'open_output_file': interface.c:2178:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, FILENAMELEN, stdin); ^ interface.c:2189:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, FILENAMELEN, stdin); ^ interface.c: In function 'create_parameter_output': interface.c:3871:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, FILENAMELEN, stdin); ^ interface.c: In function 'new_sequence_align': interface.c:2431:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, MAXLINE, stdin); ^ interface.c: In function 'get_tree': interface.c:2667:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, MAXLINE, stdin); ^ interface.c: In function 'profile_align': interface.c:2811:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, MAXLINE, stdin); ^ interface.c:2840:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(temp, MAXLINE, stdin); ^ mpicc -c -g sequence.c sequence.c: In function 'get_clustal_seq': sequence.c:158:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ^ sequence.c:163:30: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for(i=1;i= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: building package `clustalw-mpi-dbgsym' in `../clustalw-mpi-dbgsym_0.15-3build1_arm64.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 118 pkgstriptranslations: processing clustalw-mpi (in debian/clustalw-mpi); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/clustalw-mpi/DEBIAN/control, package clustalw-mpi, directory debian/clustalw-mpi pkgstripfiles: PNG optimization for package clustalw-mpi took 0 s dpkg-deb: warning: 'debian/clustalw-mpi/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `clustalw-mpi' in `../clustalw-mpi_0.15-3build1_arm64.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../clustalw-mpi_0.15-3build1_arm64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build clustalw-mpi-0.15 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131215-0748 Publishing debug debs. chroot-autobuild/build/buildd/clustalw-mpi_0.15-3build1_arm64.deb: new debian package, version 2.0. size 120780 bytes: control archive=1359 bytes. 1780 bytes, 37 lines control 599 bytes, 8 lines md5sums Package: clustalw-mpi Version: 0.15-3build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 312 Depends: libc6 (>= 2.17), libmpich10 Suggests: seaview, clustalx Enhances: clustalw Section: non-free/science Priority: optional Homepage: http://www.bii.a-star.edu.sg/achievements/applications/clustalw/ Description: MPI-distributed global sequence alignment with ClustalW ClustalW is a popular tool for multiple sequence alignment. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is an MPI implementation of ClustalW. Based on version 1.82 of the original ClustalW, both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard. The pairwise alignments can be easily parallelized since the many alignments are time independent on each other. However the progressive alignments are essentially not parallelizable because of the time dependencies between each alignment. . Here the recursive parallelism paradigm is applied to the linear space profile-profile alignment algorithm. This approach is more time efficient on computers with distributed memory architecture. Traditional approach that relies on precomputing the profile-profile score matrix has also been implemented. Results shown the latter is indeed more appropriate for shared memory multiprocessor computer. . ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments. . The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/ chroot-autobuild/build/buildd/clustalw-mpi_0.15-3build1_arm64.deb: drwxr-xr-x root/root 0 2013-12-15 07:48 ./ drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/ drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/bin/ -rwxr-xr-x root/root 251752 2013-12-15 07:48 ./usr/bin/clustalw-mpi drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/ drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/doc/clustalw-mpi/ -rw-r--r-- root/root 1994 2008-05-23 07:36 ./usr/share/doc/clustalw-mpi/History -rw-r--r-- root/root 1903 2013-09-08 00:21 ./usr/share/doc/clustalw-mpi/copyright drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/doc/clustalw-mpi/examples/ -rw-r--r-- root/root 3834 2003-04-07 01:33 ./usr/share/doc/clustalw-mpi/examples/dele.input.gz -rw-r--r-- root/root 12960 2003-04-07 01:33 ./usr/share/doc/clustalw-mpi/examples/db10.input.gz -rw-r--r-- root/root 1949 2013-12-15 06:04 ./usr/share/doc/clustalw-mpi/changelog.Debian.gz -rw-r--r-- root/root 2602 2008-05-23 07:37 ./usr/share/doc/clustalw-mpi/README.clustalw-mpi.gz drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/man/ drwxr-xr-x root/root 0 2013-12-15 07:48 ./usr/share/man/man1/ -rw-r--r-- root/root 596 2013-12-15 07:48 ./usr/share/man/man1/clustalw-mpi.1.gz clustalw-mpi_0.15-3build1_arm64.changes: Format: 1.8 Date: Sun, 15 Dec 2013 01:04:18 -0500 Source: clustalw-mpi Binary: clustalw-mpi Architecture: arm64 Version: 0.15-3build1 Distribution: trusty-proposed Urgency: medium Maintainer: Ubuntu Build Daemon Changed-By: Logan Rosen Description: clustalw-mpi - MPI-distributed global sequence alignment with ClustalW Changes: clustalw-mpi (0.15-3build1) trusty; urgency=medium . * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. Checksums-Sha1: 13faf39bf42e15b806b5953ceb10fc4b8f6d4fb3 120780 clustalw-mpi_0.15-3build1_arm64.deb Checksums-Sha256: 5d660ccb3e957cfd078536e4aaa2c9ed443d2b3fe17ff0d7a5dede7c85907c31 120780 clustalw-mpi_0.15-3build1_arm64.deb Files: d1f9909bb87bb336309bcaab62838da5 120780 non-free/science optional clustalw-mpi_0.15-3build1_arm64.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131215-0748 Build needed 00:00:39, 3848k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5337386'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5337386/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5337386'] Unmounting chroot for build PACKAGEBUILD-5337386... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5337386'] Removing build PACKAGEBUILD-5337386