RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux komainu 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_119~0.IS.08.04 python-lpbuildd_119~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 15 Dec 03:52:24 ntpdate[935]: adjust time server 10.211.37.1 offset 0.000111 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5337023', '/home/buildd/filecache-default/bbd96c485e13ab8d985945617c0760e05eb3f309'] Unpacking chroot for build PACKAGEBUILD-5337023 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5337023'] Mounting chroot for build PACKAGEBUILD-5337023 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5337023', '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-5337023 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5337023', 'amd64'] Updating debian chroot for build PACKAGEBUILD-5337023 Ign http://ftpmaster.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://ftpmaster.internal trusty-updates InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty-proposed InRelease Ign http://archive-team.internal trusty Release.gpg Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Get:2 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:3 http://archive-team.internal trusty Release [730 B] Get:4 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal trusty Release [58.5 kB] Get:7 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:8 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:9 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:10 http://archive-team.internal trusty/main amd64 Packages Ign http://archive-team.internal trusty/main Translation-en Get:11 http://ftpmaster.internal trusty/main amd64 Packages [1264 kB] Get:12 http://ftpmaster.internal trusty/restricted amd64 Packages [11.5 kB] Get:13 http://ftpmaster.internal trusty/universe amd64 Packages [5802 kB] Get:14 http://ftpmaster.internal trusty/multiverse amd64 Packages [132 kB] Get:15 http://ftpmaster.internal trusty/main Translation-en [729 kB] Get:16 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:17 http://ftpmaster.internal trusty/restricted Translation-en [3433 B] Get:18 http://ftpmaster.internal trusty/universe Translation-en [3998 kB] Get:19 http://ftpmaster.internal trusty-security/main amd64 Packages [14 B] Get:20 http://ftpmaster.internal trusty-security/restricted amd64 Packages [14 B] Get:21 http://ftpmaster.internal trusty-security/universe amd64 Packages [14 B] Get:22 http://ftpmaster.internal trusty-security/multiverse amd64 Packages [14 B] Get:23 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:24 http://ftpmaster.internal trusty-security/multiverse Translation-en [14 B] Get:25 http://ftpmaster.internal trusty-security/restricted Translation-en [14 B] Get:26 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:27 http://ftpmaster.internal trusty-updates/main amd64 Packages [14 B] Get:28 http://ftpmaster.internal trusty-updates/restricted amd64 Packages [14 B] Get:29 http://ftpmaster.internal trusty-updates/universe amd64 Packages [14 B] Get:30 http://ftpmaster.internal trusty-updates/multiverse amd64 Packages [14 B] Get:31 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:32 http://ftpmaster.internal trusty-updates/multiverse Translation-en [14 B] Get:33 http://ftpmaster.internal trusty-updates/restricted Translation-en [14 B] Get:34 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:35 http://ftpmaster.internal trusty-proposed/main amd64 Packages [26.6 kB] Get:36 http://ftpmaster.internal trusty-proposed/restricted amd64 Packages [14 B] Get:37 http://ftpmaster.internal trusty-proposed/universe amd64 Packages [252 kB] Get:38 http://ftpmaster.internal trusty-proposed/multiverse amd64 Packages [5632 B] Get:39 http://ftpmaster.internal trusty-proposed/main Translation-en [13.7 kB] Get:40 http://ftpmaster.internal trusty-proposed/multiverse Translation-en [3408 B] Get:41 http://ftpmaster.internal trusty-proposed/restricted Translation-en [14 B] Get:42 http://ftpmaster.internal trusty-proposed/universe Translation-en [125 kB] Fetched 12.7 MB in 4s (2857 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 libasan0 libatomic1 libcomerr2 libdb5.3 libfakeroot libgcc-4.8-dev libgcc1 libgcrypt11 libgomp1 libitm1 liblockfile-bin liblockfile1 libplymouth2 libquadmath0 libsqlite3-0 libss2 libstdc++-4.8-dev libstdc++6 libtsan0 linux-libc-dev perl perl-base perl-modules plymouth sed tar 42 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 33.5 MB of archives. After this operation, 1024 B disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs amd64 1.42.8-1ubuntu3 [179 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs amd64 1.42.8-1ubuntu3 [642 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main hostname amd64 3.15ubuntu1 [11.3 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-proposed/main perl amd64 5.18.1-5 [2629 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty-proposed/main perl-base amd64 5.18.1-5 [1147 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-proposed/main libdb5.3 amd64 5.3.28-3ubuntu1 [647 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main sed amd64 4.2.2-2ubuntu2 [139 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main tar amd64 1.27-4 [196 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libitm1 amd64 4.8.2-10ubuntu1 [28.5 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 amd64 4.8.2-10ubuntu1 [23.1 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libasan0 amd64 4.8.2-10ubuntu1 [63.1 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base amd64 4.8.2-10ubuntu1 [14.8 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 amd64 1:4.8.2-10ubuntu1 [37.5 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 amd64 4.8.2-10ubuntu1 [8632 B] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libtsan0 amd64 4.8.2-10ubuntu1 [94.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libquadmath0 amd64 4.8.2-10ubuntu1 [126 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 amd64 4.8.2-10ubuntu1 [4446 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev amd64 4.8.2-10ubuntu1 [1050 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 amd64 4.8.2-10ubuntu1 [7020 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 amd64 4.8.2-10ubuntu1 [4952 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev amd64 4.8.2-10ubuntu1 [1688 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 amd64 4.8.2-10ubuntu1 [251 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main binutils amd64 2.24-2ubuntu1 [2067 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libapt-pkg4.12 amd64 0.9.14.1ubuntu1 [628 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main apt amd64 0.9.14.1ubuntu1 [951 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 amd64 1.42.8-1ubuntu3 [61.2 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main libss2 amd64 1.42.8-1ubuntu3 [65.5 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgcrypt11 amd64 1.5.3-2ubuntu2 [237 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main liblockfile-bin amd64 1.09-6ubuntu1 [10.8 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main liblockfile1 amd64 1.09-6ubuntu1 [8056 B] Get:32 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libsqlite3-0 amd64 3.8.1-1ubuntu3 [336 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main plymouth amd64 0.8.8-0ubuntu12 [98.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main libplymouth2 amd64 0.8.8-0ubuntu12 [76.4 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main apt-transport-https amd64 0.9.14.1ubuntu1 [24.7 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main cpp amd64 4:4.8.2-1ubuntu2 [27.7 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main gcc amd64 4:4.8.2-1ubuntu2 [5006 B] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main g++ amd64 4:4.8.2-1ubuntu2 [1490 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty-proposed/main build-essential amd64 11.6ubuntu6 [4838 B] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libfakeroot amd64 1.20-3ubuntu1 [25.3 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main fakeroot amd64 1.20-3ubuntu1 [55.1 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main linux-libc-dev amd64 3.12.0-7.15 [727 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.5 MB in 2s (15.4 MB/s) (Reading database ... 11978 files and directories currently installed.) Preparing to replace e2fslibs:amd64 1.42.8-1ubuntu1 (using .../e2fslibs_1.42.8-1ubuntu3_amd64.deb) ... Unpacking replacement e2fslibs:amd64 ... Setting up e2fslibs:amd64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace e2fsprogs 1.42.8-1ubuntu1 (using .../e2fsprogs_1.42.8-1ubuntu3_amd64.deb) ... Unpacking replacement e2fsprogs ... Setting up e2fsprogs (1.42.8-1ubuntu3) ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace hostname 3.13ubuntu1 (using .../hostname_3.15ubuntu1_amd64.deb) ... Unpacking replacement hostname ... Setting up hostname (3.15ubuntu1) ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace perl 5.18.1-4build1 (using .../perl_5.18.1-5_amd64.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.18.1-4build1 (using .../perl-base_5.18.1-5_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.18.1-5) ... (Reading database ... 11978 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 libdb5.3:amd64 5.3.28-3 (using .../libdb5.3_5.3.28-3ubuntu1_amd64.deb) ... Unpacking replacement libdb5.3:amd64 ... Setting up libdb5.3:amd64 (5.3.28-3ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace sed 4.2.2-2ubuntu1 (using .../sed_4.2.2-2ubuntu2_amd64.deb) ... Unpacking replacement sed ... Setting up sed (4.2.2-2ubuntu2) ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace tar 1.27-3 (using .../archives/tar_1.27-4_amd64.deb) ... Unpacking replacement tar ... Setting up tar (1.27-4) ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace libitm1:amd64 4.8.2-1ubuntu2 (using .../libitm1_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libitm1:amd64 ... Preparing to replace libgomp1:amd64 4.8.2-1ubuntu2 (using .../libgomp1_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libgomp1:amd64 ... Preparing to replace libasan0:amd64 4.8.2-1ubuntu2 (using .../libasan0_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libasan0:amd64 ... Preparing to replace gcc-4.8-base:amd64 4.8.2-1ubuntu2 (using .../gcc-4.8-base_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement gcc-4.8-base:amd64 ... Setting up gcc-4.8-base:amd64 (4.8.2-10ubuntu1) ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace libgcc1:amd64 1:4.8.2-1ubuntu2 (using .../libgcc1_1%3a4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libgcc1:amd64 ... Setting up libgcc1:amd64 (1:4.8.2-10ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11978 files and directories currently installed.) Preparing to replace libatomic1:amd64 4.8.2-1ubuntu2 (using .../libatomic1_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libatomic1:amd64 ... Preparing to replace libtsan0:amd64 4.8.2-1ubuntu2 (using .../libtsan0_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libtsan0:amd64 ... Preparing to replace libquadmath0:amd64 4.8.2-1ubuntu2 (using .../libquadmath0_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libquadmath0:amd64 ... Preparing to replace cpp-4.8 4.8.2-1ubuntu2 (using .../cpp-4.8_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement cpp-4.8 ... Preparing to replace libstdc++-4.8-dev:amd64 4.8.2-1ubuntu2 (using .../libstdc++-4.8-dev_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libstdc++-4.8-dev:amd64 ... Preparing to replace g++-4.8 4.8.2-1ubuntu2 (using .../g++-4.8_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement g++-4.8 ... Preparing to replace gcc-4.8 4.8.2-1ubuntu2 (using .../gcc-4.8_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement gcc-4.8 ... Preparing to replace libgcc-4.8-dev:amd64 4.8.2-1ubuntu2 (using .../libgcc-4.8-dev_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libgcc-4.8-dev:amd64 ... Preparing to replace libstdc++6:amd64 4.8.2-1ubuntu2 (using .../libstdc++6_4.8.2-10ubuntu1_amd64.deb) ... Unpacking replacement libstdc++6:amd64 ... Setting up libstdc++6:amd64 (4.8.2-10ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11977 files and directories currently installed.) Preparing to replace binutils 2.24-1ubuntu2 (using .../binutils_2.24-2ubuntu1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libapt-pkg4.12:amd64 0.9.13.1~ubuntu1 (using .../libapt-pkg4.12_0.9.14.1ubuntu1_amd64.deb) ... Unpacking replacement libapt-pkg4.12:amd64 ... Setting up libapt-pkg4.12:amd64 (0.9.14.1ubuntu1) ... Processing triggers for libc-bin ... (Reading database ... 11977 files and directories currently installed.) Preparing to replace apt 0.9.13.1~ubuntu1 (using .../apt_0.9.14.1ubuntu1_amd64.deb) ... Unpacking replacement apt ... Setting up apt (0.9.14.1ubuntu1) ... (Reading database ... 11977 files and directories currently installed.) Preparing to replace libcomerr2:amd64 1.42.8-1ubuntu1 (using .../libcomerr2_1.42.8-1ubuntu3_amd64.deb) ... Unpacking replacement libcomerr2:amd64 ... Setting up libcomerr2:amd64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11977 files and directories currently installed.) Preparing to replace libss2:amd64 1.42.8-1ubuntu1 (using .../libss2_1.42.8-1ubuntu3_amd64.deb) ... Unpacking replacement libss2:amd64 ... Setting up libss2:amd64 (1.42.8-1ubuntu3) ... Processing triggers for libc-bin ... (Reading database ... 11977 files and directories currently installed.) Preparing to replace libgcrypt11:amd64 1.5.3-2ubuntu1 (using .../libgcrypt11_1.5.3-2ubuntu2_amd64.deb) ... Unpacking replacement libgcrypt11:amd64 ... Preparing to replace liblockfile-bin 1.09-6 (using .../liblockfile-bin_1.09-6ubuntu1_amd64.deb) ... Unpacking replacement liblockfile-bin ... Preparing to replace liblockfile1:amd64 1.09-6 (using .../liblockfile1_1.09-6ubuntu1_amd64.deb) ... Unpacking replacement liblockfile1:amd64 ... Preparing to replace libsqlite3-0:amd64 3.8.1-1ubuntu1 (using .../libsqlite3-0_3.8.1-1ubuntu3_amd64.deb) ... Unpacking replacement libsqlite3-0:amd64 ... Preparing to replace plymouth 0.8.8-0ubuntu11 (using .../plymouth_0.8.8-0ubuntu12_amd64.deb) ... Unpacking replacement plymouth ... Preparing to replace libplymouth2:amd64 0.8.8-0ubuntu11 (using .../libplymouth2_0.8.8-0ubuntu12_amd64.deb) ... Unpacking replacement libplymouth2:amd64 ... Preparing to replace apt-transport-https 0.9.13.1~ubuntu1 (using .../apt-transport-https_0.9.14.1ubuntu1_amd64.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace cpp 4:4.8.1-2ubuntu3 (using .../cpp_4%3a4.8.2-1ubuntu2_amd64.deb) ... Unpacking replacement cpp ... Preparing to replace gcc 4:4.8.1-2ubuntu3 (using .../gcc_4%3a4.8.2-1ubuntu2_amd64.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_amd64.deb) ... Unpacking replacement g++ ... Preparing to replace build-essential 11.6ubuntu5 (using .../build-essential_11.6ubuntu6_amd64.deb) ... Unpacking replacement build-essential ... Preparing to replace libfakeroot:amd64 1.20-3 (using .../libfakeroot_1.20-3ubuntu1_amd64.deb) ... Unpacking replacement libfakeroot:amd64 ... Preparing to replace fakeroot 1.20-3 (using .../fakeroot_1.20-3ubuntu1_amd64.deb) ... Unpacking replacement fakeroot ... Preparing to replace linux-libc-dev:amd64 3.12.0-5.13 (using .../linux-libc-dev_3.12.0-7.15_amd64.deb) ... Unpacking replacement linux-libc-dev:amd64 ... Setting up libitm1:amd64 (4.8.2-10ubuntu1) ... Setting up libgomp1:amd64 (4.8.2-10ubuntu1) ... Setting up libasan0:amd64 (4.8.2-10ubuntu1) ... Setting up libatomic1:amd64 (4.8.2-10ubuntu1) ... Setting up libtsan0:amd64 (4.8.2-10ubuntu1) ... Setting up libquadmath0:amd64 (4.8.2-10ubuntu1) ... Setting up cpp-4.8 (4.8.2-10ubuntu1) ... Setting up libgcc-4.8-dev:amd64 (4.8.2-10ubuntu1) ... Setting up libstdc++-4.8-dev:amd64 (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:amd64 (1.5.3-2ubuntu2) ... Setting up liblockfile-bin (1.09-6ubuntu1) ... Setting up liblockfile1:amd64 (1.09-6ubuntu1) ... Setting up libsqlite3-0:amd64 (3.8.1-1ubuntu3) ... Setting up libplymouth2:amd64 (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:amd64 (1.20-3ubuntu1) ... Setting up fakeroot (1.20-3ubuntu1) ... Setting up linux-libc-dev:amd64 (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-5337023', 'amd64', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '--purpose=PRIMARY', '--architecture=amd64', '--comp=multiverse', 'abyss_1.3.6-1build1.dsc'] Initiating build PACKAGEBUILD-5337023 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Automatic build of abyss_1.3.6-1build1 on komainu by sbuild/amd64 1.170.5 Build started at 20131215-0353 ****************************************************************************** abyss_1.3.6-1build1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), autotools-dev, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev Checking for already installed source dependencies... debhelper: missing autotools-dev: missing libboost-graph-dev: missing libopenmpi-dev: missing libsparsehash-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev libboost-graph-dev libopenmpi-dev libsparsehash-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 groff-base intltool-debian libasprintf0c2 libboost-graph1.54-dev libboost-graph1.54.0 libboost-regex1.54.0 libboost-serialization1.54-dev libboost-serialization1.54.0 libboost-test1.54-dev libboost-test1.54.0 libboost1.54-dev libcr0 libcroco3 libexpat1 libglib2.0-0 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu48 libltdl7 libmagic1 libnuma1 libopenmpi1.6 libpci-dev libpci3 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libtorque2 libunistring0 libxml2 libxml2-dev man-db mime-support openmpi-common po-debconf python3 python3-minimal python3.3 python3.3-minimal zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff graphviz libboost1.54-doc libboost-atomic1.54-dev libboost-chrono1.54-dev libboost-context1.54-dev libboost-coroutine.54-dev libboost-date-time1.54-dev libboost-exception1.54-dev libboost-filesystem1.54-dev libboost-graph-parallel1.54-dev libboost-iostreams1.54-dev libboost-locale1.54-dev libboost-log.54-dev libboost-math1.54-dev libboost-mpi1.54-dev libboost-mpi-python1.54-dev libboost-program-options1.54-dev libboost-python1.54-dev libboost-random1.54-dev libboost-regex1.54-dev libboost-signals1.54-dev libboost-system1.54-dev libboost-thread1.54-dev libboost-timer1.54-dev libboost-wave1.54-dev libbost1.54-tools-dev blcr-dkms libhwloc-contrib-plugins pkg-config 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 libhwloc-plugins xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof autotools-dev bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libboost-graph-dev libboost-graph1.54-dev libboost-graph1.54.0 libboost-regex1.54.0 libboost-serialization1.54-dev libboost-serialization1.54.0 libboost-test1.54-dev libboost-test1.54.0 libboost1.54-dev libcr0 libcroco3 libexpat1 libglib2.0-0 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu48 libltdl7 libmagic1 libnuma1 libopenmpi-dev libopenmpi1.6 libpci-dev libpci3 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libsparsehash-dev libssl1.0.0 libtorque2 libunistring0 libxml2 libxml2-dev man-db mime-support openmpi-common po-debconf python3 python3-minimal python3.3 python3.3-minimal zlib1g-dev 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 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Get:1 http://ftpmaster.internal/ubuntu/ trusty/main libexpat1 amd64 2.1.0-4ubuntu1 [71.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main libmagic1 amd64 1:5.14-2ubuntu1 [183 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libssl1.0.0 amd64 1.0.1e-4ubuntu3 [826 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-minimal amd64 3.3.3-4 [394 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-stdlib amd64 3.3.3-4 [2055 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main python3.3-minimal amd64 3.3.3-4 [1375 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main libasprintf0c2 amd64 0.18.3.1-1ubuntu1 [7244 B] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libglib2.0-0 amd64 2.39.1-0ubuntu3 [1040 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libnuma1 amd64 2.0.9~rc5-1ubuntu1 [20.3 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libpci3 amd64 1:3.1.9-6ubuntu11 [25.1 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 amd64 1.2.5-1 [23.7 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libxml2 amd64 2.9.1+dfsg1-3ubuntu3 [571 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main groff-base amd64 1.22.2-3 [719 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main man-db amd64 2.6.5-2 [710 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main libicu48 amd64 4.8.1.1-13+nmu1ubuntu1 [4725 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main libboost-regex1.54.0 amd64 1.54.0-4~ubuntu4 [261 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/universe libboost-graph1.54.0 amd64 1.54.0-4~ubuntu4 [94.9 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libboost-serialization1.54.0 amd64 1.54.0-4~ubuntu4 [126 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libboost-test1.54.0 amd64 1.54.0-4~ubuntu4 [178 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libltdl7 amd64 2.4.2-1.3ubuntu2 [35.3 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu2 [270 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/universe libhwloc5 amd64 1.8-1 [77.9 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main python3.3 amd64 3.3.3-4 [129 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main python3-minimal amd64 3.3.2-17 [26.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main libpython3-stdlib amd64 3.3.2-17 [7864 B] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main python3 amd64 3.3.2-17 [9196 B] Get:30 http://ftpmaster.internal/ubuntu/ trusty-proposed/main dh-python all 1.20131021-1ubuntu3 [50.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main file amd64 1:5.14-2ubuntu1 [18.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main gettext-base amd64 0.18.3.1-1ubuntu1 [78.9 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main gettext amd64 0.18.3.1-1ubuntu1 [1033 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu35 [20.1 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu35 [7300 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131127ubuntu1 [604 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libboost1.54-dev amd64 1.54.0-4~ubuntu4 [5662 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main libboost-serialization1.54-dev amd64 1.54.0-4~ubuntu4 [152 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main libboost-test1.54-dev amd64 1.54.0-4~ubuntu4 [213 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/universe libboost-graph1.54-dev amd64 1.54.0-4~ubuntu4 [98.4 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/universe libboost-graph-dev amd64 1.54.0.1ubuntu1 [2912 B] Get:45 http://ftpmaster.internal/ubuntu/ trusty/universe libcr0 amd64 0.8.5-2.1 [18.6 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main libpci-dev amd64 1:3.1.9-6ubuntu11 [43.6 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main libsparsehash-dev all 1.10-1ubuntu1 [111 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/universe libtorque2 amd64 2.4.16+dfsg-1ubuntu1 [90.9 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main libxml2-dev amd64 2.9.1+dfsg1-3ubuntu3 [629 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty-proposed/universe openmpi-common all 1.6.5-6ubuntu1 [101 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/universe libhwloc-dev amd64 1.8-1 [130 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libibverbs1 amd64 1.1.6-1ubuntu2 [27.8 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libibverbs-dev amd64 1.1.6-1ubuntu2 [76.7 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-proposed/universe libopenmpi1.6 amd64 1.6.5-6ubuntu1 [1394 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty-proposed/universe libopenmpi-dev amd64 1.6.5-6ubuntu1 [379 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.7 MB in 1s (14.2 MB/s) Selecting previously unselected package libexpat1:amd64. 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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'. Setting up libicu48:amd64 (4.8.1.1-13+nmu1ubuntu1) ... Setting up libboost-regex1.54.0:amd64 (1.54.0-4~ubuntu4) ... Setting up libboost-graph1.54.0:amd64 (1.54.0-4~ubuntu4) ... Setting up libboost-serialization1.54.0:amd64 (1.54.0-4~ubuntu4) ... Setting up libboost-test1.54.0:amd64 (1.54.0-4~ubuntu4) ... Setting up libcroco3:amd64 (0.6.8-2ubuntu1) ... Setting up libltdl7:amd64 (2.4.2-1.3ubuntu2) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu2) ... Setting up libhwloc5:amd64 (1.8-1) ... Setting up python3.3 (3.3.3-4) ... Setting up python3-minimal (3.3.2-17) ... Setting up libpython3-stdlib:amd64 (3.3.2-17) ... 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Setting up libibverbs-dev (1.1.6-1ubuntu2) ... Setting up libopenmpi1.6 (1.6.5-6ubuntu1) ... Setting up libopenmpi-dev (1.6.5-6ubuntu1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode 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 03:44:37 2013 UTC using RSA key ID EA330543 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./abyss_1.3.6-1build1.dsc dpkg-source: info: extracting abyss in abyss-1.3.6 dpkg-source: info: unpacking abyss_1.3.6.orig.tar.gz dpkg-source: info: unpacking abyss_1.3.6-1build1.debian.tar.gz dpkg-source: info: applying abyss-pe dpkg-source: info: applying gcc4.8.patch dpkg-buildpackage: source package abyss dpkg-buildpackage: source version 1.3.6-1build1 dpkg-buildpackage: source distribution trusty dpkg-source --before-build abyss-1.3.6 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build-arch dh build-arch dh_testdir -a debian/rules override_dh_auto_configure make[1]: Entering directory `/build/buildd/abyss-1.3.6' dh_auto_configure -- --with-mpi=/usr/lib/openmpi --disable-popcnt configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-popcnt checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for ghc... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -E checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... no checking unordered_map presence... no checking for unordered_map... no checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking for g++ option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Misc/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-popcnt make[1]: Leaving directory `/build/buildd/abyss-1.3.6' debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/abyss-1.3.6' dh_auto_build --parallel make[2]: Entering directory `/build/buildd/abyss-1.3.6' make all-recursive make[3]: Entering directory `/build/buildd/abyss-1.3.6' Making all in bin make[4]: Entering directory `/build/buildd/abyss-1.3.6/bin' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/bin' Making all in doc make[4]: Entering directory `/build/buildd/abyss-1.3.6/doc' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/doc' Making all in Assembly make[4]: Entering directory `/build/buildd/abyss-1.3.6/Assembly' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo './'`AssemblyAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo './'`BranchGroup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo './'`BranchRecord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo './'`DotWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo './'`SequenceCollection.cpp rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-BranchGroup.o libassembly_a-BranchRecord.o libassembly_a-DotWriter.o libassembly_a-Options.o libassembly_a-SequenceCollection.o ranlib libassembly.a make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Assembly' Making all in Common make[4]: Entering directory `/build/buildd/abyss-1.3.6/Common' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-SeqExt.o `test -f 'SeqExt.cpp' || echo './'`SeqExt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-SeqExt.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ranlib libcommon.a make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Common' Making all in DataLayer make[4]: Entering directory `/build/buildd/abyss-1.3.6/DataLayer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ranlib libdatalayer.a g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DataLayer' Making all in FMIndex make[4]: Entering directory `/build/buildd/abyss-1.3.6/FMIndex' g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ranlib libfmindex.a g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/FMIndex' Making all in Graph make[4]: Entering directory `/build/buildd/abyss-1.3.6/Graph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libgraph_a-ConstrainedSearch.o `test -f 'ConstrainedSearch.cpp' || echo './'`ConstrainedSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc rm -f libgraph.a ar cru libgraph.a libgraph_a-ConstrainedSearch.o ranlib libgraph.a g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L. -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-todot abyss_todot-todot.o libgraph.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Graph' Making all in dialign make[4]: Entering directory `/build/buildd/abyss-1.3.6/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o translate.o translate.c io.c: In function 'read_scr_matrix': io.c:270:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%i", &is); ^ io.c:282:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%s\n", rline); ^ io.c: In function 'read_diag_prob_dist': io.c:371:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^ gcc -DHAVE_CONFIG_H -I. -I.. -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o museq.o museq.c rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ranlib libdialign.a gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/dialign' Making all in Align make[4]: Entering directory `/build/buildd/abyss-1.3.6/Align' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ranlib libalign.a g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Align' Making all in ABYSS make[4]: Entering directory `/build/buildd/abyss-1.3.6/ABYSS' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo './'`Abyss.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ABYSS ABYSS-Abyss.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/ABYSS' Making all in Parallel make[4]: Entering directory `/build/buildd/abyss-1.3.6/Parallel' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a -lmpi -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Parallel' Making all in AdjList make[4]: Entering directory `/build/buildd/abyss-1.3.6/AdjList' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AdjList AdjList-AdjList.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/AdjList' Making all in Consensus make[4]: Entering directory `/build/buildd/abyss-1.3.6/Consensus' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Consensus' Making all in DAssembler make[4]: Entering directory `/build/buildd/abyss-1.3.6/DAssembler' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DAssembler' Making all in DistanceEst make[4]: Entering directory `/build/buildd/abyss-1.3.6/DistanceEst' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DistanceEst' Making all in KAligner make[4]: Entering directory `/build/buildd/abyss-1.3.6/KAligner' g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -pthread -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/KAligner' Making all in Layout make[4]: Entering directory `/build/buildd/abyss-1.3.6/Layout' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Layout' Making all in Map make[4]: Entering directory `/build/buildd/abyss-1.3.6/Map' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Map' Making all in MergePaths make[4]: Entering directory `/build/buildd/abyss-1.3.6/MergePaths' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MergeContigs MergeContigs-MergeContigs.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MergePaths MergePaths-MergePaths.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../Graph/libgraph.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/MergePaths' Making all in Misc make[4]: Entering directory `/build/buildd/abyss-1.3.6/Misc' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Misc' Making all in Overlap make[4]: Entering directory `/build/buildd/abyss-1.3.6/Overlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Overlap Overlap-Overlap.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Overlap' Making all in ParseAligns make[4]: Entering directory `/build/buildd/abyss-1.3.6/ParseAligns' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/ParseAligns' Making all in PathOverlap make[4]: Entering directory `/build/buildd/abyss-1.3.6/PathOverlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PathOverlap PathOverlap-PathOverlap.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/PathOverlap' Making all in PopBubbles make[4]: Entering directory `/build/buildd/abyss-1.3.6/PopBubbles' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PopBubbles PopBubbles-PopBubbles.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/PopBubbles' Making all in Scaffold make[4]: Entering directory `/build/buildd/abyss-1.3.6/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-scaffold abyss_scaffold-scaffold.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Scaffold' Making all in SimpleGraph make[4]: Entering directory `/build/buildd/abyss-1.3.6/SimpleGraph' g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wno-strict-aliasing -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -Wno-strict-aliasing -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -pthread -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o SimpleGraph SimpleGraph-SimpleGraph.o ../Graph/libgraph.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/SimpleGraph' Making all in kmerprint make[4]: Entering directory `/build/buildd/abyss-1.3.6/kmerprint' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/kmerprint' Making all in FilterGraph make[4]: Entering directory `/build/buildd/abyss-1.3.6/FilterGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo './'`FilterGraph.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory `/build/buildd/abyss-1.3.6/FilterGraph' make[4]: Entering directory `/build/buildd/abyss-1.3.6' make[4]: Leaving directory `/build/buildd/abyss-1.3.6' make[3]: Leaving directory `/build/buildd/abyss-1.3.6' make[2]: Leaving directory `/build/buildd/abyss-1.3.6' make[1]: Leaving directory `/build/buildd/abyss-1.3.6' dh_auto_test -a make[1]: Entering directory `/build/buildd/abyss-1.3.6' Making check in bin make[2]: Entering directory `/build/buildd/abyss-1.3.6/bin' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/bin' Making check in doc make[2]: Entering directory `/build/buildd/abyss-1.3.6/doc' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/doc' Making check in Assembly make[2]: Entering directory `/build/buildd/abyss-1.3.6/Assembly' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Assembly' Making check in Common make[2]: Entering directory `/build/buildd/abyss-1.3.6/Common' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Common' Making check in DataLayer make[2]: Entering directory `/build/buildd/abyss-1.3.6/DataLayer' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/DataLayer' Making check in FMIndex make[2]: Entering directory `/build/buildd/abyss-1.3.6/FMIndex' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/FMIndex' Making check in Graph make[2]: Entering directory `/build/buildd/abyss-1.3.6/Graph' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Graph' Making check in dialign make[2]: Entering directory `/build/buildd/abyss-1.3.6/dialign' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/dialign' Making check in Align make[2]: Entering directory `/build/buildd/abyss-1.3.6/Align' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Align' Making check in ABYSS make[2]: Entering directory `/build/buildd/abyss-1.3.6/ABYSS' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/ABYSS' Making check in Parallel make[2]: Entering directory `/build/buildd/abyss-1.3.6/Parallel' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Parallel' Making check in AdjList make[2]: Entering directory `/build/buildd/abyss-1.3.6/AdjList' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/AdjList' Making check in Consensus make[2]: Entering directory `/build/buildd/abyss-1.3.6/Consensus' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Consensus' Making check in DAssembler make[2]: Entering directory `/build/buildd/abyss-1.3.6/DAssembler' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/DAssembler' Making check in DistanceEst make[2]: Entering directory `/build/buildd/abyss-1.3.6/DistanceEst' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/DistanceEst' Making check in KAligner make[2]: Entering directory `/build/buildd/abyss-1.3.6/KAligner' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/KAligner' Making check in Layout make[2]: Entering directory `/build/buildd/abyss-1.3.6/Layout' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Layout' Making check in Map make[2]: Entering directory `/build/buildd/abyss-1.3.6/Map' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Map' Making check in MergePaths make[2]: Entering directory `/build/buildd/abyss-1.3.6/MergePaths' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/MergePaths' Making check in Misc make[2]: Entering directory `/build/buildd/abyss-1.3.6/Misc' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Misc' Making check in Overlap make[2]: Entering directory `/build/buildd/abyss-1.3.6/Overlap' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Overlap' Making check in ParseAligns make[2]: Entering directory `/build/buildd/abyss-1.3.6/ParseAligns' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/ParseAligns' Making check in PathOverlap make[2]: Entering directory `/build/buildd/abyss-1.3.6/PathOverlap' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/PathOverlap' Making check in PopBubbles make[2]: Entering directory `/build/buildd/abyss-1.3.6/PopBubbles' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/PopBubbles' Making check in Scaffold make[2]: Entering directory `/build/buildd/abyss-1.3.6/Scaffold' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/Scaffold' Making check in SimpleGraph make[2]: Entering directory `/build/buildd/abyss-1.3.6/SimpleGraph' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/SimpleGraph' Making check in kmerprint make[2]: Entering directory `/build/buildd/abyss-1.3.6/kmerprint' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/kmerprint' Making check in FilterGraph make[2]: Entering directory `/build/buildd/abyss-1.3.6/FilterGraph' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/abyss-1.3.6/FilterGraph' make[2]: Entering directory `/build/buildd/abyss-1.3.6' make[2]: Leaving directory `/build/buildd/abyss-1.3.6' make[1]: Leaving directory `/build/buildd/abyss-1.3.6' /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/abyss-1.3.6' dh_auto_install --destdir=debian/tmp make[2]: Entering directory `/build/buildd/abyss-1.3.6' Making install in bin make[3]: Entering directory `/build/buildd/abyss-1.3.6/bin' make[4]: Entering directory `/build/buildd/abyss-1.3.6/bin' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/bin' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/bin' Making install in doc make[3]: Entering directory `/build/buildd/abyss-1.3.6/doc' make[4]: Entering directory `/build/buildd/abyss-1.3.6/doc' make[4]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/man/man1' make[4]: Leaving directory `/build/buildd/abyss-1.3.6/doc' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/doc' Making install in Assembly make[3]: Entering directory `/build/buildd/abyss-1.3.6/Assembly' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Assembly' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Assembly' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Assembly' Making install in Common make[3]: Entering directory `/build/buildd/abyss-1.3.6/Common' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Common' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Common' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Common' Making install in DataLayer make[3]: Entering directory `/build/buildd/abyss-1.3.6/DataLayer' make[4]: Entering directory `/build/buildd/abyss-1.3.6/DataLayer' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DataLayer' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/DataLayer' Making install in FMIndex make[3]: Entering directory `/build/buildd/abyss-1.3.6/FMIndex' make[4]: Entering directory `/build/buildd/abyss-1.3.6/FMIndex' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/FMIndex' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/FMIndex' Making install in Graph make[3]: Entering directory `/build/buildd/abyss-1.3.6/Graph' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Graph' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Graph' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Graph' Making install in dialign make[3]: Entering directory `/build/buildd/abyss-1.3.6/dialign' make[4]: Entering directory `/build/buildd/abyss-1.3.6/dialign' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/dialign' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/dialign' Making install in Align make[3]: Entering directory `/build/buildd/abyss-1.3.6/Align' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Align' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Align' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Align' Making install in ABYSS make[3]: Entering directory `/build/buildd/abyss-1.3.6/ABYSS' make[4]: Entering directory `/build/buildd/abyss-1.3.6/ABYSS' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/ABYSS' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/ABYSS' Making install in Parallel make[3]: Entering directory `/build/buildd/abyss-1.3.6/Parallel' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Parallel' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Parallel' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Parallel' Making install in AdjList make[3]: Entering directory `/build/buildd/abyss-1.3.6/AdjList' make[4]: Entering directory `/build/buildd/abyss-1.3.6/AdjList' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/AdjList' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/AdjList' Making install in Consensus make[3]: Entering directory `/build/buildd/abyss-1.3.6/Consensus' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Consensus' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Consensus' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Consensus' Making install in DAssembler make[3]: Entering directory `/build/buildd/abyss-1.3.6/DAssembler' make[4]: Entering directory `/build/buildd/abyss-1.3.6/DAssembler' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DAssembler' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/DAssembler' Making install in DistanceEst make[3]: Entering directory `/build/buildd/abyss-1.3.6/DistanceEst' make[4]: Entering directory `/build/buildd/abyss-1.3.6/DistanceEst' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/DistanceEst' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/DistanceEst' Making install in KAligner make[3]: Entering directory `/build/buildd/abyss-1.3.6/KAligner' make[4]: Entering directory `/build/buildd/abyss-1.3.6/KAligner' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/KAligner' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/KAligner' Making install in Layout make[3]: Entering directory `/build/buildd/abyss-1.3.6/Layout' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Layout' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Layout' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Layout' Making install in Map make[3]: Entering directory `/build/buildd/abyss-1.3.6/Map' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Map' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-overlap '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Map' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Map' Making install in MergePaths make[3]: Entering directory `/build/buildd/abyss-1.3.6/MergePaths' make[4]: Entering directory `/build/buildd/abyss-1.3.6/MergePaths' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/MergePaths' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/MergePaths' Making install in Misc make[3]: Entering directory `/build/buildd/abyss-1.3.6/Misc' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Misc' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Misc' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Misc' Making install in Overlap make[3]: Entering directory `/build/buildd/abyss-1.3.6/Overlap' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Overlap' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Overlap' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Overlap' Making install in ParseAligns make[3]: Entering directory `/build/buildd/abyss-1.3.6/ParseAligns' make[4]: Entering directory `/build/buildd/abyss-1.3.6/ParseAligns' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate ParseAligns '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/ParseAligns' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/ParseAligns' Making install in PathOverlap make[3]: Entering directory `/build/buildd/abyss-1.3.6/PathOverlap' make[4]: Entering directory `/build/buildd/abyss-1.3.6/PathOverlap' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/PathOverlap' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/PathOverlap' Making install in PopBubbles make[3]: Entering directory `/build/buildd/abyss-1.3.6/PopBubbles' make[4]: Entering directory `/build/buildd/abyss-1.3.6/PopBubbles' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/PopBubbles' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/PopBubbles' Making install in Scaffold make[3]: Entering directory `/build/buildd/abyss-1.3.6/Scaffold' make[4]: Entering directory `/build/buildd/abyss-1.3.6/Scaffold' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/Scaffold' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/Scaffold' Making install in SimpleGraph make[3]: Entering directory `/build/buildd/abyss-1.3.6/SimpleGraph' make[4]: Entering directory `/build/buildd/abyss-1.3.6/SimpleGraph' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/SimpleGraph' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/SimpleGraph' Making install in kmerprint make[3]: Entering directory `/build/buildd/abyss-1.3.6/kmerprint' make[4]: Entering directory `/build/buildd/abyss-1.3.6/kmerprint' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/kmerprint' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/kmerprint' Making install in FilterGraph make[3]: Entering directory `/build/buildd/abyss-1.3.6/FilterGraph' make[4]: Entering directory `/build/buildd/abyss-1.3.6/FilterGraph' /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/buildd/abyss-1.3.6/debian/tmp/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/abyss-1.3.6/FilterGraph' make[3]: Leaving directory `/build/buildd/abyss-1.3.6/FilterGraph' make[3]: Entering directory `/build/buildd/abyss-1.3.6' make[4]: Entering directory `/build/buildd/abyss-1.3.6' make[4]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog COPYRIGHT LICENSE README.css README.html README.md '/build/buildd/abyss-1.3.6/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory `/build/buildd/abyss-1.3.6' make[3]: Leaving directory `/build/buildd/abyss-1.3.6' make[2]: Leaving directory `/build/buildd/abyss-1.3.6' make[1]: Leaving directory `/build/buildd/abyss-1.3.6' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: abyss dh_strip debug symbol extraction: packages to act on: abyss dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: building package `abyss-dbgsym' in `../abyss-dbgsym_1.3.6-1build1_amd64.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 abyss (in debian/abyss); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/abyss/DEBIAN/control, package abyss, directory debian/abyss pkgstripfiles: Truncating usr/share/doc/abyss/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package abyss took 0 s dpkg-deb: warning: 'debian/abyss/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `abyss' in `../abyss_1.3.6-1build1_amd64.deb'. dpkg-genchanges -B -mUbuntu/amd64 Build Daemon >../abyss_1.3.6-1build1_amd64.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 abyss-1.3.6 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131215-0357 Publishing debug debs. chroot-autobuild/build/buildd/abyss_1.3.6-1build1_amd64.deb: new debian package, version 2.0. size 855402 bytes: control archive= 2093 bytes. 968 bytes, 21 lines control 2949 bytes, 48 lines md5sums Package: abyss Version: 1.3.6-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3983 Depends: make, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libopenmpi1.6, libstdc++6 (>= 4.4.0), perl Suggests: openmpi-bin Section: non-free/science Priority: optional Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. . To cite your use of ABySS, please reference ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June. chroot-autobuild/build/buildd/abyss_1.3.6-1build1_amd64.deb: drwxr-xr-x root/root 0 2013-12-15 03:57 ./ drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/ drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/bin/ -rwxr-xr-x root/root 11740 2013-12-15 03:56 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/lib/ drwxr-xr-x root/root 0 2013-12-15 03:57 ./usr/lib/abyss/ -rwxr-xr-x root/root 76896 2013-12-15 03:57 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 84976 2013-12-15 03:57 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 60424 2013-12-15 03:57 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 1192 2013-12-15 03:56 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 85072 2013-12-15 03:57 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 125960 2013-12-15 03:57 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 290288 2013-12-15 03:57 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 121896 2013-12-15 03:57 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 286168 2013-12-15 03:57 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 85088 2013-12-15 03:57 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 11740 2013-12-15 03:56 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 72664 2013-12-15 03:57 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 265800 2013-12-15 03:57 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 4455 2013-12-15 03:56 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 187656 2013-12-15 03:57 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 171336 2013-12-15 03:57 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 1135 2013-12-15 03:56 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 154912 2013-12-15 03:57 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 1208 2013-12-15 03:56 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1280 2013-12-15 03:56 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 113760 2013-12-15 03:57 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 220568 2013-12-15 03:57 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 138400 2013-12-15 03:57 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 105520 2013-12-15 03:57 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 97344 2013-12-15 03:57 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 154880 2013-12-15 03:57 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 72816 2013-12-15 03:57 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 89096 2013-12-15 03:57 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 191896 2013-12-15 03:57 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 93272 2013-12-15 03:57 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 76896 2013-12-15 03:57 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 113712 2013-12-15 03:57 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 1362 2013-12-15 03:56 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 39 2013-12-15 03:56 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 109728 2013-12-15 03:57 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 126144 2013-12-15 03:57 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 113664 2013-12-15 03:57 ./usr/lib/abyss/PathOverlap drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/share/ drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/share/doc/abyss/ -rw-r--r-- root/root 4445 2013-07-31 22:12 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 704 2013-02-04 21:45 ./usr/share/doc/abyss/README.css -rw-r--r-- root/root 1106 2013-12-15 03:57 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 669 2013-09-08 02:23 ./usr/share/doc/abyss/README.Debian -rw-r--r-- root/root 18533 2013-09-08 02:32 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66145 2013-03-07 22:43 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 16221 2013-07-31 23:39 ./usr/share/doc/abyss/README.html drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/share/man/ drwxr-xr-x root/root 0 2013-12-15 03:56 ./usr/share/man/man1/ -rw-r--r-- root/root 1178 2013-12-15 03:56 ./usr/share/man/man1/ABYSS.1.gz -rw-r--r-- root/root 407 2013-12-15 03:56 ./usr/share/man/man1/abyss-tofastq.1.gz -rw-r--r-- root/root 2328 2013-12-15 03:56 ./usr/share/man/man1/abyss-pe.1.gz abyss_1.3.6-1build1_amd64.changes: Format: 1.8 Date: Sat, 14 Dec 2013 22:43:43 -0500 Source: abyss Binary: abyss Architecture: amd64 Version: 1.3.6-1build1 Distribution: trusty-proposed Urgency: medium Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Logan Rosen Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.6-1build1) trusty; urgency=medium . * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. Checksums-Sha1: c2af04f3f2dbb3279a7c7409155c3a77cb7123c7 855402 abyss_1.3.6-1build1_amd64.deb Checksums-Sha256: 729e4f065eae90bf672c31c741ac7a84a7b2a74494d9067f489267311bd0073a 855402 abyss_1.3.6-1build1_amd64.deb Files: f4b3f76bf95db9ae8cc4fc66749ed648 855402 non-free/science optional abyss_1.3.6-1build1_amd64.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131215-0357 Build needed 00:02:41, 188508k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5337023'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5337023/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5337023'] Unmounting chroot for build PACKAGEBUILD-5337023... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5337023'] Removing build PACKAGEBUILD-5337023