RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux fisher03 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_124~0.IS.08.04 python-lpbuildd_124~0.IS.08.04 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 24 Oct 23:22:41 ntpdate[12863]: adjust time server 10.211.37.1 offset -0.000022 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6486155', '/home/buildd/filecache-default/0ef1c011ee7ed9eb33dd33237ba11b0bf82afae6'] Unpacking chroot for build PACKAGEBUILD-6486155 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6486155'] Mounting chroot for build PACKAGEBUILD-6486155 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6486155', 'deb http://ftpmaster.internal/ubuntu vivid main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu vivid-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu vivid-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu vivid-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-6486155 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6486155', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-6486155 Ign http://ftpmaster.internal vivid InRelease Ign http://archive-team.internal vivid InRelease Ign http://ftpmaster.internal vivid-security InRelease Ign http://archive-team.internal vivid Release.gpg Ign http://ftpmaster.internal vivid-updates InRelease Get:1 http://archive-team.internal vivid Release [742 B] Ign http://ftpmaster.internal vivid-proposed InRelease Get:2 http://ftpmaster.internal vivid Release.gpg [933 B] Get:3 http://ftpmaster.internal vivid-security Release.gpg [933 B] Get:4 http://ftpmaster.internal vivid-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal vivid-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal vivid Release [112 kB] Get:7 http://archive-team.internal vivid/main ppc64el Packages Get:8 http://ftpmaster.internal vivid-security Release [59.7 kB] Ign http://archive-team.internal vivid/main Translation-en Get:9 http://ftpmaster.internal vivid-updates Release [59.7 kB] Get:10 http://ftpmaster.internal vivid-proposed Release [59.7 kB] Get:11 http://ftpmaster.internal vivid/main ppc64el Packages [1280 kB] Get:12 http://ftpmaster.internal vivid/restricted ppc64el Packages [14 B] Get:13 http://ftpmaster.internal vivid/universe ppc64el Packages [5898 kB] Get:14 http://ftpmaster.internal vivid/multiverse ppc64el Packages [110 kB] Get:15 http://ftpmaster.internal vivid/main Translation-en [769 kB] Get:16 http://ftpmaster.internal vivid/multiverse Translation-en [101 kB] Get:17 http://ftpmaster.internal vivid/restricted Translation-en [3315 B] Get:18 http://ftpmaster.internal vivid/universe Translation-en [4275 kB] Get:19 http://ftpmaster.internal vivid-security/main ppc64el Packages [14 B] Get:20 http://ftpmaster.internal vivid-security/restricted ppc64el Packages [14 B] Get:21 http://ftpmaster.internal vivid-security/universe ppc64el Packages [14 B] Get:22 http://ftpmaster.internal vivid-security/multiverse ppc64el Packages [14 B] Get:23 http://ftpmaster.internal vivid-security/main Translation-en [14 B] Get:24 http://ftpmaster.internal vivid-security/multiverse Translation-en [14 B] Get:25 http://ftpmaster.internal vivid-security/restricted Translation-en [14 B] Get:26 http://ftpmaster.internal vivid-security/universe Translation-en [14 B] Get:27 http://ftpmaster.internal vivid-updates/main ppc64el Packages [14 B] Get:28 http://ftpmaster.internal vivid-updates/restricted ppc64el Packages [14 B] Get:29 http://ftpmaster.internal vivid-updates/universe ppc64el Packages [14 B] Get:30 http://ftpmaster.internal vivid-updates/multiverse ppc64el Packages [14 B] Get:31 http://ftpmaster.internal vivid-updates/main Translation-en [14 B] Get:32 http://ftpmaster.internal vivid-updates/multiverse Translation-en [14 B] Get:33 http://ftpmaster.internal vivid-updates/restricted Translation-en [14 B] Get:34 http://ftpmaster.internal vivid-updates/universe Translation-en [14 B] Get:35 http://ftpmaster.internal vivid-proposed/main ppc64el Packages [25.4 kB] Get:36 http://ftpmaster.internal vivid-proposed/restricted ppc64el Packages [14 B] Get:37 http://ftpmaster.internal vivid-proposed/universe ppc64el Packages [211 kB] Get:38 http://ftpmaster.internal vivid-proposed/multiverse ppc64el Packages [1772 B] Get:39 http://ftpmaster.internal vivid-proposed/main Translation-en [19.0 kB] Get:40 http://ftpmaster.internal vivid-proposed/multiverse Translation-en [4895 B] Get:41 http://ftpmaster.internal vivid-proposed/restricted Translation-en [14 B] Get:42 http://ftpmaster.internal vivid-proposed/universe Translation-en [141 kB] Fetched 13.1 MB in 8s (1479 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils ca-certificates cpp-4.9 g++-4.9 gcc-4.9 gcc-4.9-base grep libacl1 libatomic1 libdb5.3 libgcc-4.9-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libplymouth4 libsasl2-2 libsasl2-modules-db libstdc++-4.9-dev libstdc++6 libsystemd-journal0 libudev1 plymouth tzdata udev 31 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 29.4 MB of archives. After this operation, 262 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main base-files ppc64el 7.2ubuntu8 [60.4 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main grep ppc64el 2.20-4 [139 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9-base ppc64el 4.9.1-19ubuntu1 [15.7 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++6 ppc64el 4.9.1-19ubuntu1 [297 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgomp1 ppc64el 4.9.1-19ubuntu1 [36.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libitm1 ppc64el 4.9.1-19ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libatomic1 ppc64el 4.9.1-19ubuntu1 [8234 B] Get:8 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc-4.9-dev ppc64el 4.9.1-19ubuntu1 [266 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid-proposed/main cpp-4.9 ppc64el 4.9.1-19ubuntu1 [4775 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid-proposed/main binutils ppc64el 2.24.90.20141023-1ubuntu1 [2173 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9 ppc64el 4.9.1-19ubuntu1 [5194 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid-proposed/main g++-4.9 ppc64el 4.9.1-19ubuntu1 [12.2 MB] Get:13 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++-4.9-dev ppc64el 4.9.1-19ubuntu1 [1129 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc1 ppc64el 1:4.9.1-19ubuntu1 [29.3 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/main libgmp10 ppc64el 2:6.0.0+dfsg-6 [223 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main libacl1 ppc64el 2.2.52-2 [15.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid/main libdb5.3 ppc64el 5.3.28-6 [633 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgpg-error0 ppc64el 1.17-1 [34.4 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsystemd-journal0 ppc64el 215-5ubuntu1 [55.2 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main plymouth ppc64el 0.9.0-0ubuntu8 [95.9 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid-proposed/main udev ppc64el 215-5ubuntu1 [855 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libudev1 ppc64el 215-5ubuntu1 [34.4 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main libplymouth4 ppc64el 0.9.0-0ubuntu8 [81.2 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main libgssapi-krb5-2 ppc64el 1.12.1+dfsg-11 [109 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5-3 ppc64el 1.12.1+dfsg-11 [265 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5support0 ppc64el 1.12.1+dfsg-11 [29.8 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main libk5crypto3 ppc64el 1.12.1+dfsg-11 [101 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-modules-db ppc64el 2.1.26.dfsg1-12 [14.2 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-2 ppc64el 2.1.26.dfsg1-12 [48.2 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main tzdata all 2014i-1 [182 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main ca-certificates all 20141019 [192 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.4 MB in 9s (3237 kB/s) (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu8_ppc64el.deb ... Unpacking base-files (7.2ubuntu8) over (7.2ubuntu7) ... Setting up base-files (7.2ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../grep_2.20-4_ppc64el.deb ... Unpacking grep (2.20-4) over (2.20-3) ... Setting up grep (2.20-4) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../gcc-4.9-base_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking gcc-4.9-base:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up gcc-4.9-base:ppc64el (4.9.1-19ubuntu1) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libstdc++6:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up libstdc++6:ppc64el (4.9.1-19ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgomp1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgomp1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libitm1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libitm1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libatomic1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libatomic1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libgcc-4.9-dev_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgcc-4.9-dev:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../cpp-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking cpp-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../binutils_2.24.90.20141023-1ubuntu1_ppc64el.deb ... Unpacking binutils (2.24.90.20141023-1ubuntu1) over (2.24.90.20141014-0ubuntu3) ... Preparing to unpack .../gcc-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking gcc-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../g++-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking g++-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libstdc++-4.9-dev_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libstdc++-4.9-dev:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libgcc1_1%3a4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgcc1:ppc64el (1:4.9.1-19ubuntu1) over (1:4.9.1-16ubuntu6) ... Setting up libgcc1:ppc64el (1:4.9.1-19ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.0.0+dfsg-6_ppc64el.deb ... Unpacking libgmp10:ppc64el (2:6.0.0+dfsg-6) over (2:6.0.0+dfsg-4build1) ... Preparing to unpack .../libacl1_2.2.52-2_ppc64el.deb ... Unpacking libacl1:ppc64el (2.2.52-2) over (2.2.52-1.1) ... Setting up libacl1:ppc64el (2.2.52-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28-6_ppc64el.deb ... Unpacking libdb5.3:ppc64el (5.3.28-6) over (5.3.28-5) ... Setting up libdb5.3:ppc64el (5.3.28-6) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.17-1_ppc64el.deb ... Unpacking libgpg-error0:ppc64el (1.17-1) over (1.13-4) ... Setting up libgpg-error0:ppc64el (1.17-1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libsystemd-journal0_215-5ubuntu1_ppc64el.deb ... Unpacking libsystemd-journal0:ppc64el (215-5ubuntu1) over (208-8ubuntu8) ... Setting up libsystemd-journal0:ppc64el (215-5ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../plymouth_0.9.0-0ubuntu8_ppc64el.deb ... Unpacking plymouth (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../udev_215-5ubuntu1_ppc64el.deb ... Unpacking udev (215-5ubuntu1) over (208-8ubuntu8) ... Preparing to unpack .../libudev1_215-5ubuntu1_ppc64el.deb ... Unpacking libudev1:ppc64el (215-5ubuntu1) over (208-8ubuntu8) ... Preparing to unpack .../libplymouth4_0.9.0-0ubuntu8_ppc64el.deb ... Unpacking libplymouth4:ppc64el (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libgssapi-krb5-2:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5-3_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libkrb5-3:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5support0_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libk5crypto3_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libk5crypto3:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-12_ppc64el.deb ... Unpacking libsasl2-modules-db:ppc64el (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-12_ppc64el.deb ... Unpacking libsasl2-2:ppc64el (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../tzdata_2014i-1_all.deb ... Unpacking tzdata (2014i-1) over (2014h-2) ... Setting up tzdata (2014i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 25 03:23:09 UTC 2014. Universal Time is now: Sat Oct 25 03:23:09 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11391 files and directories currently installed.) Preparing to unpack .../ca-certificates_20141019_all.deb ... Unpacking ca-certificates (20141019) over (20140325) ... Setting up libgomp1:ppc64el (4.9.1-19ubuntu1) ... Setting up libitm1:ppc64el (4.9.1-19ubuntu1) ... Setting up libatomic1:ppc64el (4.9.1-19ubuntu1) ... Setting up libgcc-4.9-dev:ppc64el (4.9.1-19ubuntu1) ... Setting up libgmp10:ppc64el (2:6.0.0+dfsg-6) ... Setting up cpp-4.9 (4.9.1-19ubuntu1) ... Setting up binutils (2.24.90.20141023-1ubuntu1) ... Setting up gcc-4.9 (4.9.1-19ubuntu1) ... Setting up libstdc++-4.9-dev:ppc64el (4.9.1-19ubuntu1) ... Setting up g++-4.9 (4.9.1-19ubuntu1) ... Setting up libudev1:ppc64el (215-5ubuntu1) ... Setting up libplymouth4:ppc64el (0.9.0-0ubuntu8) ... Setting up udev (215-5ubuntu1) ... Installing new version of config file /etc/init.d/udev-finish ... A chroot environment has been detected, udev not started. update-initramfs: deferring update (trigger activated) Removing obsolete conffile /etc/udev/rules.d/README ... Setting up plymouth (0.9.0-0ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up libkrb5support0:ppc64el (1.12.1+dfsg-11) ... Setting up libk5crypto3:ppc64el (1.12.1+dfsg-11) ... Setting up libkrb5-3:ppc64el (1.12.1+dfsg-11) ... Setting up libgssapi-krb5-2:ppc64el (1.12.1+dfsg-11) ... Setting up libsasl2-modules-db:ppc64el (2.1.26.dfsg1-12) ... Setting up libsasl2-2:ppc64el (2.1.26.dfsg1-12) ... Setting up ca-certificates (20141019) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for initramfs-tools (0.103ubuntu8) ... Processing triggers for ca-certificates (20141019) ... Updating certificates in /etc/ssl/certs... 10 added, 5 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6486155', 'ppc64el', 'vivid-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=vivid-proposed', '--purpose=PRIMARY', '--architecture=ppc64el', '--comp=multiverse', 'abyss_1.5.2-1.dsc'] Initiating build PACKAGEBUILD-6486155 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Automatic build of abyss_1.5.2-1 on fisher03 by sbuild/ppc64el 1.170.5 Build started at 20141024-2323 ****************************************************************************** abyss_1.5.2-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), dh-autoreconf, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev Checking for already installed source dependencies... debhelper: missing dh-autoreconf: missing libboost-graph-dev: missing libopenmpi-dev: missing libsparsehash-dev: missing libtext-multimarkdown-perl: missing libgtest-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper dh-autoreconf libboost-graph-dev libopenmpi-dev libsparsehash-dev libtext-multimarkdown-perl libgtest-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils dh-apparmor file gettext gettext-base groff-base intltool-debian libasprintf0c2 libboost-graph1.55-dev libboost-graph1.55.0 libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-test1.55-dev libboost-test1.55.0 libboost1.55-dev libcroco3 libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu52 libltdl7 libmagic1 libopenmpi1.6 libpci-dev libpci3 libpipeline1 libsigsegv2 libtext-markdown-perl libtool libtorque2 libunistring0 liburi-perl libxml2 libxml2-dev m4 man-db openmpi-common po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff graphviz libboost1.55-doc libboost-atomic1.55-dev libboost-chrono1.55-dev libboost-context1.55-dev libboost-coroutine1.55-dev libboost-date-time1.55-dev libboost-exception1.55-dev libboost-filesystem1.55-dev libboost-graph-parallel1.55-dev libboost-iostreams1.55-dev libboost-locale1.55-dev libboost-log1.55-dev libboost-math1.55-dev libboost-mpi1.55-dev libboost-mpi-python1.55-dev libboost-program-options1.55-dev libboost-python1.55-dev libboost-random1.55-dev libboost-regex1.55-dev libboost-signals1.55-dev libboost-system1.55-dev libboost-thread1.55-dev libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev libmpfrc++-dev libntl-dev libdata-dump-perl libhwloc-contrib-plugins libtool-doc automaken gfortran fortran95-compiler gcj-jdk libwww-perl pkg-config less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-apparmor dh-autoreconf file gettext gettext-base groff-base intltool-debian libasprintf0c2 libboost-graph-dev libboost-graph1.55-dev libboost-graph1.55.0 libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-test1.55-dev libboost-test1.55.0 libboost1.55-dev libcroco3 libglib2.0-0 libgtest-dev libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu52 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpci-dev libpci3 libpipeline1 libsigsegv2 libsparsehash-dev libtext-markdown-perl libtext-multimarkdown-perl libtool libtorque2 libunistring0 liburi-perl libxml2 libxml2-dev m4 man-db openmpi-common po-debconf zlib1g-dev 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 25.5 MB of archives. After this operation, 189 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main libmagic1 ppc64el 1:5.19-1ubuntu1.1 [206 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main libasprintf0c2 ppc64el 0.19.2-2ubuntu1 [6352 B] Get:3 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-0 ppc64el 2.42.0-2 [1024 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid/main libpci3 ppc64el 1:3.2.1-1ubuntu9 [22.2 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid/main libpipeline1 ppc64el 1.3.1-1 [23.5 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libxml2 ppc64el 2.9.1+dfsg1-4ubuntu1 [617 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid/main groff-base ppc64el 1.22.2-8 [1385 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid/main bsdmainutils ppc64el 9.0.5ubuntu1 [173 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid/main man-db ppc64el 2.7.0.2-2 [852 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid/main libicu52 ppc64el 52.1-6 [6902 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid/main libboost-regex1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [249 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [93.3 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid/main libboost-serialization1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [126 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid/main libboost-test1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [168 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/main libcroco3 ppc64el 0.6.8-3 [77.2 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main libltdl7 ppc64el 2.4.2-1.11 [38.2 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid/main libsigsegv2 ppc64el 2.10-4 [13.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid/main libunistring0 ppc64el 0.9.3-5ubuntu3 [262 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid/universe libhwloc5 ppc64el 1.8-1ubuntu1 [62.9 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main file ppc64el 1:5.19-1ubuntu1.1 [20.4 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main gettext-base ppc64el 0.19.2-2ubuntu1 [46.5 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main m4 ppc64el 1.4.17-4 [194 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main autoconf all 2.69-8 [321 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main autotools-dev all 20140911.1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main automake all 1:1.14.1-3ubuntu1 [510 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main autopoint all 0.19.2-2ubuntu1 [383 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main gettext ppc64el 0.19.2-2ubuntu1 [866 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main po-debconf all 1.0.16+nmu3 [207 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main dh-apparmor all 2.8.98-0ubuntu2 [11.0 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main debhelper all 9.20141003ubuntu1 [726 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid/main libtool all 2.4.2-1.11 [180 kB] Get:33 http://ftpmaster.internal/ubuntu/ vivid/main dh-autoreconf all 10 [15.3 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main libboost1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [5801 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/main libboost-serialization1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [157 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid/main libboost-test1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [226 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [102 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph-dev ppc64el 1.55.0.1~ubuntu1 [2966 B] Get:39 http://ftpmaster.internal/ubuntu/ vivid/main libgtest-dev ppc64el 1.7.0-3 [198 kB] Get:40 http://ftpmaster.internal/ubuntu/ vivid/main liburi-perl all 1.64-1 [84.1 kB] Get:41 http://ftpmaster.internal/ubuntu/ vivid/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:42 http://ftpmaster.internal/ubuntu/ vivid/main libhtml-parser-perl ppc64el 3.71-1build2 [95.8 kB] Get:43 http://ftpmaster.internal/ubuntu/ vivid/main zlib1g-dev ppc64el 1:1.2.8.dfsg-1ubuntu1 [166 kB] Get:44 http://ftpmaster.internal/ubuntu/ vivid/main libpci-dev ppc64el 1:3.2.1-1ubuntu9 [40.9 kB] Get:45 http://ftpmaster.internal/ubuntu/ vivid/main libsparsehash-dev all 2.0.2-1 [72.4 kB] Get:46 http://ftpmaster.internal/ubuntu/ vivid/universe libtext-markdown-perl all 1.0.26-1 [36.5 kB] Get:47 http://ftpmaster.internal/ubuntu/ vivid/universe libtext-multimarkdown-perl all 1.000035-1 [24.8 kB] Get:48 http://ftpmaster.internal/ubuntu/ vivid/universe libtorque2 ppc64el 2.4.16+dfsg-1.4ubuntu1 [72.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ vivid/main libxml2-dev ppc64el 2.9.1+dfsg1-4ubuntu1 [707 kB] Get:50 http://ftpmaster.internal/ubuntu/ vivid/universe openmpi-common all 1.6.5-8 [101 kB] Get:51 http://ftpmaster.internal/ubuntu/ vivid/universe libhwloc-dev ppc64el 1.8-1ubuntu1 [121 kB] Get:52 http://ftpmaster.internal/ubuntu/ vivid/main libibverbs1 ppc64el 1.1.8-1ubuntu1 [23.7 kB] Get:53 http://ftpmaster.internal/ubuntu/ vivid/main libibverbs-dev ppc64el 1.1.8-1ubuntu1 [77.8 kB] Get:54 http://ftpmaster.internal/ubuntu/ vivid/universe libopenmpi1.6 ppc64el 1.6.5-8 [1193 kB] Get:55 http://ftpmaster.internal/ubuntu/ vivid/universe libopenmpi-dev ppc64el 1.6.5-8 [380 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.5 MB in 17s (1440 kB/s) Selecting previously unselected package libmagic1:ppc64el. (Reading database ... 11396 files and directories currently installed.) Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1.1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.19-1ubuntu1.1) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.19.2-2ubuntu1_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.19.2-2ubuntu1) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../libglib2.0-0_2.42.0-2_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.42.0-2) ... Selecting previously unselected package libpci3:ppc64el. Preparing to unpack .../libpci3_1%3a3.2.1-1ubuntu9_ppc64el.deb ... Unpacking libpci3:ppc64el (1:3.2.1-1ubuntu9) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../libpipeline1_1.3.1-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.3.1-1) ... Selecting previously unselected package libxml2:ppc64el. 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Selecting previously unselected package libboost-graph1.55.0:ppc64el. Preparing to unpack .../libboost-graph1.55.0_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-graph1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Selecting previously unselected package libboost-serialization1.55.0:ppc64el. Preparing to unpack .../libboost-serialization1.55.0_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-serialization1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Selecting previously unselected package libboost-test1.55.0:ppc64el. Preparing to unpack .../libboost-test1.55.0_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-test1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Selecting previously unselected package libcroco3:ppc64el. Preparing to unpack .../libcroco3_0.6.8-3_ppc64el.deb ... Unpacking libcroco3:ppc64el (0.6.8-3) ... Selecting previously unselected package libltdl7:ppc64el. Preparing to unpack .../libltdl7_2.4.2-1.11_ppc64el.deb ... Unpacking libltdl7:ppc64el (2.4.2-1.11) ... Selecting previously unselected package libsigsegv2:ppc64el. Preparing to unpack .../libsigsegv2_2.10-4_ppc64el.deb ... Unpacking libsigsegv2:ppc64el (2.10-4) ... Selecting previously unselected package libunistring0:ppc64el. Preparing to unpack .../libunistring0_0.9.3-5ubuntu3_ppc64el.deb ... Unpacking libunistring0:ppc64el (0.9.3-5ubuntu3) ... Selecting previously unselected package libhwloc5:ppc64el. Preparing to unpack .../libhwloc5_1.8-1ubuntu1_ppc64el.deb ... Unpacking libhwloc5:ppc64el (1.8-1ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.19-1ubuntu1.1_ppc64el.deb ... Unpacking file (1:5.19-1ubuntu1.1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.2-2ubuntu1_ppc64el.deb ... Unpacking gettext-base (0.19.2-2ubuntu1) ... Selecting previously unselected package m4. Preparing to unpack .../m4_1.4.17-4_ppc64el.deb ... Unpacking m4 (1.4.17-4) ... 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Selecting previously unselected package liburi-perl. Preparing to unpack .../liburi-perl_1.64-1_all.deb ... Unpacking liburi-perl (1.64-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../libhtml-tagset-perl_3.20-2_all.deb ... Unpacking libhtml-tagset-perl (3.20-2) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../libhtml-parser-perl_3.71-1build2_ppc64el.deb ... Unpacking libhtml-parser-perl (3.71-1build2) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1ubuntu1_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.8.dfsg-1ubuntu1) ... Selecting previously unselected package libpci-dev. Preparing to unpack .../libpci-dev_1%3a3.2.1-1ubuntu9_ppc64el.deb ... Unpacking libpci-dev (1:3.2.1-1ubuntu9) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../libsparsehash-dev_2.0.2-1_all.deb ... Unpacking libsparsehash-dev (2.0.2-1) ... Selecting previously unselected package libtext-markdown-perl. Preparing to unpack .../libtext-markdown-perl_1.0.26-1_all.deb ... Unpacking libtext-markdown-perl (1.0.26-1) ... Selecting previously unselected package libtext-multimarkdown-perl. Preparing to unpack .../libtext-multimarkdown-perl_1.000035-1_all.deb ... Unpacking libtext-multimarkdown-perl (1.000035-1) ... Selecting previously unselected package libtorque2. Preparing to unpack .../libtorque2_2.4.16+dfsg-1.4ubuntu1_ppc64el.deb ... Unpacking libtorque2 (2.4.16+dfsg-1.4ubuntu1) ... Selecting previously unselected package libxml2-dev:ppc64el. Preparing to unpack .../libxml2-dev_2.9.1+dfsg1-4ubuntu1_ppc64el.deb ... Unpacking libxml2-dev:ppc64el (2.9.1+dfsg1-4ubuntu1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../openmpi-common_1.6.5-8_all.deb ... Unpacking openmpi-common (1.6.5-8) ... Selecting previously unselected package libhwloc-dev:ppc64el. Preparing to unpack .../libhwloc-dev_1.8-1ubuntu1_ppc64el.deb ... Unpacking libhwloc-dev:ppc64el (1.8-1ubuntu1) ... Selecting previously unselected package libibverbs1. Preparing to unpack .../libibverbs1_1.1.8-1ubuntu1_ppc64el.deb ... Unpacking libibverbs1 (1.1.8-1ubuntu1) ... Selecting previously unselected package libibverbs-dev. Preparing to unpack .../libibverbs-dev_1.1.8-1ubuntu1_ppc64el.deb ... Unpacking libibverbs-dev (1.1.8-1ubuntu1) ... Selecting previously unselected package libopenmpi1.6. Preparing to unpack .../libopenmpi1.6_1.6.5-8_ppc64el.deb ... Unpacking libopenmpi1.6 (1.6.5-8) ... Selecting previously unselected package libopenmpi-dev. Preparing to unpack .../libopenmpi-dev_1.6.5-8_ppc64el.deb ... Unpacking libopenmpi-dev (1.6.5-8) ... Setting up libmagic1:ppc64el (1:5.19-1ubuntu1.1) ... Setting up libasprintf0c2:ppc64el (0.19.2-2ubuntu1) ... Setting up libglib2.0-0:ppc64el (2.42.0-2) ... No schema files found: doing nothing. Setting up libpci3:ppc64el (1:3.2.1-1ubuntu9) ... Setting up libpipeline1:ppc64el (1.3.1-1) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-4ubuntu1) ... Setting up groff-base (1.22.2-8) ... 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 (2.7.0.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libicu52:ppc64el (52.1-6) ... Setting up libboost-regex1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-serialization1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-test1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libcroco3:ppc64el (0.6.8-3) ... Setting up libltdl7:ppc64el (2.4.2-1.11) ... Setting up libsigsegv2:ppc64el (2.10-4) ... Setting up libunistring0:ppc64el (0.9.3-5ubuntu3) ... Setting up libhwloc5:ppc64el (1.8-1ubuntu1) ... Setting up file (1:5.19-1ubuntu1.1) ... Setting up gettext-base (0.19.2-2ubuntu1) ... Setting up m4 (1.4.17-4) ... Setting up autoconf (2.69-8) ... Setting up autotools-dev (20140911.1) ... Setting up automake (1:1.14.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.2-2ubuntu1) ... Setting up gettext (0.19.2-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.98-0ubuntu2) ... Setting up debhelper (9.20141003ubuntu1) ... Setting up libtool (2.4.2-1.11) ... Setting up dh-autoreconf (10) ... Setting up libboost1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-serialization1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-test1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph-dev:ppc64el (1.55.0.1~ubuntu1) ... Setting up libgtest-dev:ppc64el (1.7.0-3) ... Setting up liburi-perl (1.64-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.71-1build2) ... Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-1ubuntu1) ... Setting up libpci-dev (1:3.2.1-1ubuntu9) ... Setting up libsparsehash-dev (2.0.2-1) ... Setting up libtext-markdown-perl (1.0.26-1) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up libtorque2 (2.4.16+dfsg-1.4ubuntu1) ... Setting up libxml2-dev:ppc64el (2.9.1+dfsg1-4ubuntu1) ... Setting up openmpi-common (1.6.5-8) ... Setting up libhwloc-dev:ppc64el (1.8-1ubuntu1) ... Setting up libibverbs1 (1.1.8-1ubuntu1) ... Setting up libibverbs-dev (1.1.8-1ubuntu1) ... Setting up libopenmpi1.6 (1.6.5-8) ... Setting up libopenmpi-dev (1.6.5-8) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Processing triggers for libc-bin (2.19-10ubuntu2) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-10ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-19ubuntu1 g++-4.9_4.9.1-19ubuntu1 binutils_2.24.90.20141023-1ubuntu1 libstdc++-4.9-dev_4.9.1-19ubuntu1 libstdc++6_4.9.1-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Fri Sep 19 20:48:09 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./abyss_1.5.2-1.dsc dpkg-source: info: extracting abyss in abyss-1.5.2 dpkg-source: info: unpacking abyss_1.5.2.orig.tar.gz dpkg-source: info: unpacking abyss_1.5.2-1.debian.tar.xz dpkg-source: info: applying abyss-pe dpkg-source: info: applying gtest.patch dpkg-source: info: applying privacy-breach.patch dpkg-buildpackage: source package abyss dpkg-buildpackage: source version 1.5.2-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build abyss-1.5.2 dpkg-buildpackage: host architecture ppc64el /usr/bin/fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_autoreconf -a configure.ac:10: installing './compile' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/buildd/abyss-1.5.2' dh_auto_configure -- --with-mpi=/usr/lib/openmpi configure: WARNING: unrecognized options: --disable-maintainer-mode 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 ghc-pkg... no ./configure: line 5184: : command not found 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 std::hash... no checking for std::tr1::hash... 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 functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes 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 unordered_set usability... no checking unordered_set presence... no checking for unordered_set... no checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking gtest/gtest.h usability... yes checking gtest/gtest.h presence... yes checking for gtest/gtest.h... yes checking for pthread_create in -lpthread... 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 Konnector/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 GapFiller/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/buildd/abyss-1.5.2' debian/rules override_dh_auto_build make[1]: Entering directory '/build/buildd/abyss-1.5.2' dh_auto_build --parallel make[2]: Entering directory '/build/buildd/abyss-1.5.2' make all-recursive make[3]: Entering directory '/build/buildd/abyss-1.5.2' Making all in bin make[4]: Entering directory '/build/buildd/abyss-1.5.2/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/bin' Making all in doc make[4]: Entering directory '/build/buildd/abyss-1.5.2/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/doc' Making all in Assembly make[4]: Entering directory '/build/buildd/abyss-1.5.2/Assembly' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/Assembly' Making all in Common make[4]: Entering directory '/build/buildd/abyss-1.5.2/Common' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/Common' Making all in DataLayer make[4]: Entering directory '/build/buildd/abyss-1.5.2/DataLayer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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-1.5.2/DataLayer' Making all in FMIndex make[4]: Entering directory '/build/buildd/abyss-1.5.2/FMIndex' g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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-1.5.2/FMIndex' Making all in Graph make[4]: Entering directory '/build/buildd/abyss-1.5.2/Graph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -Wformat -Werror=format-security -L. -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Graph' Making all in dialign make[4]: Entering directory '/build/buildd/abyss-1.5.2/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c io.c: In function 'read_scr_matrix': io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%i", &is); ^ io.c:282:5: 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:371:7: 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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c In function 'output_line_left', inlined from 'print_info' at io.c:869:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:872:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:875:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:878:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:881:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:884:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:948:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:951:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:954:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:957:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:960:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ In function 'output_line_left', inlined from 'print_info' at io.c:963:10: io.c:1116:9: warning: attempt to free a non-heap object [-Wfree-nonheap-object] free(string); ^ 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 -O3 -fstack-protector-strong -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-1.5.2/dialign' Making all in Align make[4]: Entering directory '/build/buildd/abyss-1.5.2/Align' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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-1.5.2/Align' Making all in ABYSS make[4]: Entering directory '/build/buildd/abyss-1.5.2/ABYSS' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo './'`Abyss.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/ABYSS' Making all in Parallel make[4]: Entering directory '/build/buildd/abyss-1.5.2/Parallel' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/Parallel' Making all in AdjList make[4]: Entering directory '/build/buildd/abyss-1.5.2/AdjList' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/AdjList' Making all in Bloom make[4]: Entering directory '/build/buildd/abyss-1.5.2/Bloom' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Bloom' Making all in Konnector make[4]: Entering directory '/build/buildd/abyss-1.5.2/Konnector' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Konnector' Making all in Consensus make[4]: Entering directory '/build/buildd/abyss-1.5.2/Consensus' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/Consensus' Making all in DAssembler make[4]: Entering directory '/build/buildd/abyss-1.5.2/DAssembler' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/buildd/abyss-1.5.2/DistanceEst' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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 g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/buildd/abyss-1.5.2/KAligner' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -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 -lpthread -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/KAligner' Making all in Layout make[4]: Entering directory '/build/buildd/abyss-1.5.2/Layout' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/buildd/abyss-1.5.2/LogKmerCount' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/LogKmerCount' Making all in Map make[4]: Entering directory '/build/buildd/abyss-1.5.2/Map' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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 -D SAM_SEQ_QUAL=1 -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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-1.5.2/Map' Making all in MergePaths make[4]: Entering directory '/build/buildd/abyss-1.5.2/MergePaths' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MergeContigs MergeContigs-MergeContigs.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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 -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/MergePaths' Making all in Misc make[4]: Entering directory '/build/buildd/abyss-1.5.2/Misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Misc' Making all in Overlap make[4]: Entering directory '/build/buildd/abyss-1.5.2/Overlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Overlap' Making all in ParseAligns make[4]: Entering directory '/build/buildd/abyss-1.5.2/ParseAligns' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -D SAM_SEQ_QUAL=1 -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -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-1.5.2/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/buildd/abyss-1.5.2/PathOverlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PathOverlap PathOverlap-PathOverlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/buildd/abyss-1.5.2/PopBubbles' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/buildd/abyss-1.5.2/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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 -O3 -fstack-protector-strong -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-1.5.2/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/buildd/abyss-1.5.2/SimpleGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -Wall -Wextra -Werror -Wno-strict-aliasing -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o SimpleGraph SimpleGraph-SimpleGraph.o ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/buildd/abyss-1.5.2/kmerprint' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/buildd/abyss-1.5.2/FilterGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cpp' || echo './'`FilterGraph.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/buildd/abyss-1.5.2/GapFiller' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/buildd/abyss-1.5.2/GapFiller' Making all in Unittest make[4]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make[4]: Entering directory '/build/buildd/abyss-1.5.2' multimarkdown README.md >README.html make[4]: Leaving directory '/build/buildd/abyss-1.5.2' make[3]: Leaving directory '/build/buildd/abyss-1.5.2' make[2]: Leaving directory '/build/buildd/abyss-1.5.2' make[1]: Leaving directory '/build/buildd/abyss-1.5.2' dh_auto_test -a make[1]: Entering directory '/build/buildd/abyss-1.5.2' Making check in bin make[2]: Entering directory '/build/buildd/abyss-1.5.2/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/bin' Making check in doc make[2]: Entering directory '/build/buildd/abyss-1.5.2/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/doc' Making check in Assembly make[2]: Entering directory '/build/buildd/abyss-1.5.2/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Assembly' Making check in Common make[2]: Entering directory '/build/buildd/abyss-1.5.2/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Common' Making check in DataLayer make[2]: Entering directory '/build/buildd/abyss-1.5.2/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/DataLayer' Making check in FMIndex make[2]: Entering directory '/build/buildd/abyss-1.5.2/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/FMIndex' Making check in Graph make[2]: Entering directory '/build/buildd/abyss-1.5.2/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Graph' Making check in dialign make[2]: Entering directory '/build/buildd/abyss-1.5.2/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/dialign' Making check in Align make[2]: Entering directory '/build/buildd/abyss-1.5.2/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Align' Making check in ABYSS make[2]: Entering directory '/build/buildd/abyss-1.5.2/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/ABYSS' Making check in Parallel make[2]: Entering directory '/build/buildd/abyss-1.5.2/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Parallel' Making check in AdjList make[2]: Entering directory '/build/buildd/abyss-1.5.2/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/AdjList' Making check in Bloom make[2]: Entering directory '/build/buildd/abyss-1.5.2/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Bloom' Making check in Konnector make[2]: Entering directory '/build/buildd/abyss-1.5.2/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Konnector' Making check in Consensus make[2]: Entering directory '/build/buildd/abyss-1.5.2/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Consensus' Making check in DAssembler make[2]: Entering directory '/build/buildd/abyss-1.5.2/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/buildd/abyss-1.5.2/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/buildd/abyss-1.5.2/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/KAligner' Making check in Layout make[2]: Entering directory '/build/buildd/abyss-1.5.2/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/buildd/abyss-1.5.2/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/LogKmerCount' Making check in Map make[2]: Entering directory '/build/buildd/abyss-1.5.2/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Map' Making check in MergePaths make[2]: Entering directory '/build/buildd/abyss-1.5.2/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/MergePaths' Making check in Misc make[2]: Entering directory '/build/buildd/abyss-1.5.2/Misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Misc' Making check in Overlap make[2]: Entering directory '/build/buildd/abyss-1.5.2/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Overlap' Making check in ParseAligns make[2]: Entering directory '/build/buildd/abyss-1.5.2/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/buildd/abyss-1.5.2/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/buildd/abyss-1.5.2/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/buildd/abyss-1.5.2/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/buildd/abyss-1.5.2/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/buildd/abyss-1.5.2/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/buildd/abyss-1.5.2/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/buildd/abyss-1.5.2/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2/GapFiller' Making check in Unittest make[2]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' make libgtest.a libgtest_main.a common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor Konnector_konnector make[3]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' cp /usr/src/gtest/src/gtest-all.cc . g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/src/gtest -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o libgtest_a-gtest-all.o `test -f 'gtest-all.cc' || echo './'`gtest-all.cc rm -f libgtest.a ar cru libgtest.a libgtest_a-gtest-all.o ranlib libgtest.a cp /usr/src/gtest/src/gtest_main.cc . g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/src/gtest -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o libgtest_main_a-gtest_main.o `test -f 'gtest_main.cc' || echo './'`gtest_main.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/src/gtest -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o libgtest_main_a-gtest-all.o `test -f 'gtest-all.cc' || echo './'`gtest-all.cc rm -f libgtest_main.a ar cru libgtest_main.a libgtest_main_a-gtest_main.o libgtest_main_a-gtest-all.o ranlib libgtest_main.a g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_stringutil-StringUtilTest.o `test -f 'Common/StringUtilTest.cpp' || echo './'`Common/StringUtilTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_stringutil Common/common_stringutil-StringUtilTest.o libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_histogram-HistogramTest.o `test -f 'Common/HistogramTest.cpp' || echo './'`Common/HistogramTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_histogram Common/common_histogram-HistogramTest.o libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_bitutil-BitUtilTest.o `test -f 'Common/BitUtilTest.cpp' || echo './'`Common/BitUtilTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_bitutil Common/common_bitutil-BitUtilTest.o libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_kmer-KmerTest.o `test -f 'Common/KmerTest.cpp' || echo './'`Common/KmerTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_kmer Common/common_kmer-KmerTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_sequence-Sequence.o `test -f 'Common/Sequence.cc' || echo './'`Common/Sequence.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_sequence Common/common_sequence-Sequence.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_KmerIterator-KmerIteratorTest.o `test -f 'Common/KmerIteratorTest.cpp' || echo './'`Common/KmerIteratorTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_KmerIterator Common/common_KmerIterator-KmerIteratorTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Common/common_sam-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o common_sam Common/common_sam-SAM.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Konnector/Konnector_DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Konnector_DBGBloom Konnector/Konnector_DBGBloom-DBGBloomTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Konnector_DBGBloomAlgorithms Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -Wall -Wextra -Werror -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/buildd/abyss-1.5.2 -isystem/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -isystem/build/buildd/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -c -o Konnector/Konnector_konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -Wall -Wextra -Werror -fopenmp -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Konnector_konnector Konnector/Konnector_konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a libgtest_main.a -lpthread -ldl -lm -ldl -lm make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make check-TESTS make[3]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' PASS: common_stringutil PASS: common_histogram PASS: common_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: BloomFilter PASS: Konnector_DBGBloom PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: Konnector_konnector make[5]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' ============================================================================ Testsuite summary for ABySS 1.5.2 ============================================================================ # TOTAL: 16 # PASS: 16 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make[2]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make[2]: Entering directory '/build/buildd/abyss-1.5.2' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/buildd/abyss-1.5.2' make[1]: Leaving directory '/build/buildd/abyss-1.5.2' /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --with autoreconf dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/buildd/abyss-1.5.2' dh_auto_install --destdir=debian/tmp make[2]: Entering directory '/build/buildd/abyss-1.5.2' Making install in bin make[3]: Entering directory '/build/buildd/abyss-1.5.2/bin' make[4]: Entering directory '/build/buildd/abyss-1.5.2/bin' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/bin' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/bin' Making install in doc make[3]: Entering directory '/build/buildd/abyss-1.5.2/doc' make[4]: Entering directory '/build/buildd/abyss-1.5.2/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/buildd/abyss-1.5.2/doc' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/doc' Making install in Assembly make[3]: Entering directory '/build/buildd/abyss-1.5.2/Assembly' make[4]: Entering directory '/build/buildd/abyss-1.5.2/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-1.5.2/Assembly' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Assembly' Making install in Common make[3]: Entering directory '/build/buildd/abyss-1.5.2/Common' make[4]: Entering directory '/build/buildd/abyss-1.5.2/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-1.5.2/Common' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Common' Making install in DataLayer make[3]: Entering directory '/build/buildd/abyss-1.5.2/DataLayer' make[4]: Entering directory '/build/buildd/abyss-1.5.2/DataLayer' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/DataLayer' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/DataLayer' Making install in FMIndex make[3]: Entering directory '/build/buildd/abyss-1.5.2/FMIndex' make[4]: Entering directory '/build/buildd/abyss-1.5.2/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-1.5.2/FMIndex' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/FMIndex' Making install in Graph make[3]: Entering directory '/build/buildd/abyss-1.5.2/Graph' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Graph' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Graph' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Graph' Making install in dialign make[3]: Entering directory '/build/buildd/abyss-1.5.2/dialign' make[4]: Entering directory '/build/buildd/abyss-1.5.2/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-1.5.2/dialign' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/dialign' Making install in Align make[3]: Entering directory '/build/buildd/abyss-1.5.2/Align' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Align' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Align' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Align' Making install in ABYSS make[3]: Entering directory '/build/buildd/abyss-1.5.2/ABYSS' make[4]: Entering directory '/build/buildd/abyss-1.5.2/ABYSS' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/ABYSS' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/ABYSS' Making install in Parallel make[3]: Entering directory '/build/buildd/abyss-1.5.2/Parallel' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Parallel' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Parallel' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Parallel' Making install in AdjList make[3]: Entering directory '/build/buildd/abyss-1.5.2/AdjList' make[4]: Entering directory '/build/buildd/abyss-1.5.2/AdjList' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/AdjList' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/AdjList' Making install in Bloom make[3]: Entering directory '/build/buildd/abyss-1.5.2/Bloom' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Bloom' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Bloom' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Bloom' Making install in Konnector make[3]: Entering directory '/build/buildd/abyss-1.5.2/Konnector' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Konnector' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Konnector' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Konnector' Making install in Consensus make[3]: Entering directory '/build/buildd/abyss-1.5.2/Consensus' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Consensus' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Consensus' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Consensus' Making install in DAssembler make[3]: Entering directory '/build/buildd/abyss-1.5.2/DAssembler' make[4]: Entering directory '/build/buildd/abyss-1.5.2/DAssembler' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/DAssembler' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/buildd/abyss-1.5.2/DistanceEst' make[4]: Entering directory '/build/buildd/abyss-1.5.2/DistanceEst' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/DistanceEst' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/buildd/abyss-1.5.2/KAligner' make[4]: Entering directory '/build/buildd/abyss-1.5.2/KAligner' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/KAligner' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/KAligner' Making install in Layout make[3]: Entering directory '/build/buildd/abyss-1.5.2/Layout' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Layout' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Layout' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/buildd/abyss-1.5.2/LogKmerCount' make[4]: Entering directory '/build/buildd/abyss-1.5.2/LogKmerCount' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/LogKmerCount' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/LogKmerCount' Making install in Map make[3]: Entering directory '/build/buildd/abyss-1.5.2/Map' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Map' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Map' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Map' Making install in MergePaths make[3]: Entering directory '/build/buildd/abyss-1.5.2/MergePaths' make[4]: Entering directory '/build/buildd/abyss-1.5.2/MergePaths' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/MergePaths' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/MergePaths' Making install in Misc make[3]: Entering directory '/build/buildd/abyss-1.5.2/Misc' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Misc' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Misc' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Misc' Making install in Overlap make[3]: Entering directory '/build/buildd/abyss-1.5.2/Overlap' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Overlap' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Overlap' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Overlap' Making install in ParseAligns make[3]: Entering directory '/build/buildd/abyss-1.5.2/ParseAligns' make[4]: Entering directory '/build/buildd/abyss-1.5.2/ParseAligns' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/ParseAligns' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/buildd/abyss-1.5.2/PathOverlap' make[4]: Entering directory '/build/buildd/abyss-1.5.2/PathOverlap' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/PathOverlap' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/buildd/abyss-1.5.2/PopBubbles' make[4]: Entering directory '/build/buildd/abyss-1.5.2/PopBubbles' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/PopBubbles' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/buildd/abyss-1.5.2/Scaffold' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Scaffold' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/Scaffold' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/buildd/abyss-1.5.2/SimpleGraph' make[4]: Entering directory '/build/buildd/abyss-1.5.2/SimpleGraph' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/SimpleGraph' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/buildd/abyss-1.5.2/kmerprint' make[4]: Entering directory '/build/buildd/abyss-1.5.2/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-1.5.2/kmerprint' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/buildd/abyss-1.5.2/FilterGraph' make[4]: Entering directory '/build/buildd/abyss-1.5.2/FilterGraph' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/FilterGraph' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/buildd/abyss-1.5.2/GapFiller' make[4]: Entering directory '/build/buildd/abyss-1.5.2/GapFiller' /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/buildd/abyss-1.5.2/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/buildd/abyss-1.5.2/GapFiller' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/GapFiller' Making install in Unittest make[3]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' make[4]: Entering directory '/build/buildd/abyss-1.5.2/Unittest' 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-1.5.2/Unittest' make[3]: Leaving directory '/build/buildd/abyss-1.5.2/Unittest' make[3]: Entering directory '/build/buildd/abyss-1.5.2' make[4]: Entering directory '/build/buildd/abyss-1.5.2' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog COPYRIGHT LICENSE README.css README.html README.md '/build/buildd/abyss-1.5.2/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/buildd/abyss-1.5.2' make[3]: Leaving directory '/build/buildd/abyss-1.5.2' make[2]: Leaving directory '/build/buildd/abyss-1.5.2' make[1]: Leaving directory '/build/buildd/abyss-1.5.2' 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: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: 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: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package abyss: unused substitution variable ${perl:Depends} /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `abyss-dbgsym' in `../abyss-dbgsym_1.5.2-1_ppc64el.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 121 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_1.5.2-1_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../abyss_1.5.2-1_ppc64el.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build abyss-1.5.2 dpkg-buildpackage: binary-only upload (no source included) ****************************************************************************** Build finished at 20141024-2328 Publishing debug debs. chroot-autobuild/build/buildd/abyss_1.5.2-1_ppc64el.deb: new debian package, version 2.0. size 1022372 bytes: control archive=2359 bytes. 761 bytes, 16 lines control 3569 bytes, 58 lines md5sums Package: abyss Version: 1.5.2-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5863 Depends: make, libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.9), libopenmpi1.6, libstdc++6 (>= 4.9), 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. chroot-autobuild/build/buildd/abyss_1.5.2-1_ppc64el.deb: drwxr-xr-x root/root 0 2014-10-24 23:28 ./ drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/ drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/bin/ -rwxr-xr-x root/root 14935 2014-10-24 23:27 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/lib/ drwxr-xr-x root/root 0 2014-10-24 23:28 ./usr/lib/abyss/ -rwxr-xr-x root/root 211584 2014-10-24 23:28 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 195264 2014-10-24 23:28 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 137632 2014-10-24 23:28 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 228120 2014-10-24 23:28 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 137720 2014-10-24 23:28 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 109024 2014-10-24 23:28 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 294144 2014-10-24 23:28 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 104928 2014-10-24 23:28 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 1208 2014-10-24 23:27 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 150176 2014-10-24 23:28 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 359880 2014-10-24 23:28 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 209 2014-10-24 23:27 ./usr/lib/abyss/abyss-tabtomd -rwxr-xr-x root/root 92824 2014-10-24 23:28 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 125512 2014-10-24 23:28 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 154224 2014-10-24 23:28 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 158344 2014-10-24 23:28 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 244384 2014-10-24 23:28 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 104880 2014-10-24 23:28 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 158176 2014-10-24 23:28 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 108976 2014-10-24 23:28 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 125544 2014-10-24 23:28 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 108976 2014-10-24 23:28 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 145816 2014-10-24 23:28 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 149912 2014-10-24 23:28 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 141648 2014-10-24 23:28 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 100680 2014-10-24 23:28 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 104768 2014-10-24 23:28 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 207600 2014-10-24 23:28 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 4501 2014-10-24 23:27 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 359136 2014-10-24 23:28 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 1454 2014-10-24 23:27 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 14935 2014-10-24 23:27 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 190984 2014-10-24 23:28 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 92560 2014-10-24 23:28 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 191112 2014-10-24 23:28 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 1280 2014-10-24 23:27 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 1135 2014-10-24 23:27 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 199456 2014-10-24 23:28 ./usr/lib/abyss/konnector -rwxr-xr-x root/root 76376 2014-10-24 23:28 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 137856 2014-10-24 23:28 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 1192 2014-10-24 23:27 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 96944 2014-10-24 23:28 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 92720 2014-10-24 23:28 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 1362 2014-10-24 23:27 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 39 2014-10-24 23:27 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 6491 2014-10-24 23:27 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 108976 2014-10-24 23:28 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 84592 2014-10-24 23:28 ./usr/lib/abyss/logcounter drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/share/ drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/share/man/man1/ -rw-r--r-- root/root 1200 2014-10-24 23:27 ./usr/share/man/man1/ABYSS.1.gz -rw-r--r-- root/root 407 2014-10-24 23:27 ./usr/share/man/man1/abyss-tofastq.1.gz -rw-r--r-- root/root 2636 2014-10-24 23:27 ./usr/share/man/man1/abyss-pe.1.gz drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-24 23:27 ./usr/share/doc/abyss/ -rw-r--r-- root/root 704 2014-07-09 19:15 ./usr/share/doc/abyss/README.css -rw-r--r-- root/root 18518 2014-09-19 16:41 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66778 2014-07-09 19:15 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 1268 2014-10-24 23:28 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 5789 2014-10-24 23:23 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 19993 2014-10-24 23:26 ./usr/share/doc/abyss/README.html abyss_1.5.2-1_ppc64el.changes: Format: 1.8 Date: Mon, 15 Sep 2014 14:53:24 +0200 Source: abyss Binary: abyss Architecture: ppc64el Version: 1.5.2-1 Distribution: vivid-proposed Urgency: medium Maintainer: Ubuntu Build Daemon Changed-By: Andreas Tille Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.5.2-1) unstable; urgency=medium . * New upstream version (remove applied patches) * d/watch: Moved to github * d/control+d/rules: use dh-autoreconf * d/control: Build-Depends: libtext-multimarkdown-perl * cme fix dpkg-control * d/control: Build-Depends: libgtest-dev to enable unit tests at build time * d/control: drop copy of citation info from long description * patch to make gtest work (thanks to Anthony Raymond ) * Drop privacy breach in doc Checksums-Sha1: ae1aa6766759a6aa80d5ea4d11fc69bb7e83c3d0 1022372 abyss_1.5.2-1_ppc64el.deb Checksums-Sha256: 54b944e37d1d51535f0ab503c22e4cd3910de7f761726da7aa759ffe4c653dbc 1022372 abyss_1.5.2-1_ppc64el.deb Files: 82dd219a49194a5e8d8caf60f049c1e7 1022372 non-free/science optional abyss_1.5.2-1_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20141024-2328 Build needed 00:04:34, 365064k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6486155'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6486155/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6486155'] Unmounting chroot for build PACKAGEBUILD-6486155... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6486155'] Removing build PACKAGEBUILD-6486155