RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.24-32-xen #1 SMP Thu Jul 12 14:30:40 UTC 2012 x86_64 Buildd toolchain package versions: launchpad-buildd_113~0.IS.08.04 python-lpbuildd_113~0.IS.08.04 bzr-builder_0.7.2+bzr156-0ubuntu1~1.IS.8.04 bzr_2.4.0-0ubuntu2~11.IS.8.04. Syncing the system clock with the buildd NTP service... 28 Aug 05:39:54 ntpdate[3405]: step time server 10.211.37.1 offset -1136331.073145 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '2691b68befa9717391609bc22893696d18ce25cc', '/home/buildd/filecache-default/8eacd1245734d394a672d9a8221787a881f94c87'] Uncompressing the tarball... Unpacking chroot for build 2691b68befa9717391609bc22893696d18ce25cc RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '2691b68befa9717391609bc22893696d18ce25cc'] Mounting chroot for build 2691b68befa9717391609bc22893696d18ce25cc RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '2691b68befa9717391609bc22893696d18ce25cc', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-updates main restricted universe multiverse'] Overriding sources.list in build-2691b68befa9717391609bc22893696d18ce25cc RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '2691b68befa9717391609bc22893696d18ce25cc', 'i386'] Updating debian chroot for build 2691b68befa9717391609bc22893696d18ce25cc Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ftpmaster.internal precise-security Release.gpg [198 B] Get:3 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:4 http://ftpmaster.internal precise Release [49.6 kB] Ign http://ppa.launchpad.net precise InRelease Get:5 http://ftpmaster.internal precise-security Release [49.6 kB] Get:6 http://ppa.launchpad.net precise Release.gpg [316 B] Get:7 http://ftpmaster.internal precise-updates Release [49.6 kB] Get:8 http://ppa.launchpad.net precise Release [11.9 kB] Ign http://ppa.launchpad.net precise Release Get:9 http://ftpmaster.internal precise/main i386 Packages [1274 kB] Get:10 http://ppa.launchpad.net precise/main i386 Packages [6426 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise/restricted i386 Packages [8431 B] Get:12 http://ftpmaster.internal precise/universe i386 Packages [4796 kB] Get:13 http://ftpmaster.internal precise/multiverse i386 Packages [121 kB] Get:14 http://ftpmaster.internal precise/main TranslationIndex [3706 B] Get:15 http://ftpmaster.internal precise/multiverse TranslationIndex [2676 B] Get:16 http://ftpmaster.internal precise/restricted TranslationIndex [2596 B] Get:17 http://ftpmaster.internal precise/universe TranslationIndex [2922 B] Get:18 http://ftpmaster.internal precise-security/main i386 Packages [160 kB] Get:19 http://ftpmaster.internal precise-security/restricted i386 Packages [3968 B] Get:20 http://ftpmaster.internal precise-security/universe i386 Packages [38.8 kB] Get:21 http://ftpmaster.internal precise-security/multiverse i386 Packages [1394 B] Get:22 http://ftpmaster.internal precise-security/main TranslationIndex [73 B] Get:23 http://ftpmaster.internal precise-security/multiverse TranslationIndex [71 B] Get:24 http://ftpmaster.internal precise-security/restricted TranslationIndex [71 B] Get:25 http://ftpmaster.internal precise-security/universe TranslationIndex [73 B] Get:26 http://ftpmaster.internal precise-updates/main i386 Packages [371 kB] Get:27 http://ftpmaster.internal precise-updates/restricted i386 Packages [6732 B] Get:28 http://ftpmaster.internal precise-updates/universe i386 Packages [121 kB] Get:29 http://ftpmaster.internal precise-updates/multiverse i386 Packages [2540 B] Get:30 http://ftpmaster.internal precise-updates/main TranslationIndex [3564 B] Get:31 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [2605 B] Get:32 http://ftpmaster.internal precise-updates/restricted TranslationIndex [2461 B] Get:33 http://ftpmaster.internal precise-updates/universe TranslationIndex [2850 B] Get:34 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:35 http://ftpmaster.internal precise/multiverse Translation-en [93.4 kB] Get:36 http://ftpmaster.internal precise/restricted Translation-en [2395 B] Get:37 http://ftpmaster.internal precise/universe Translation-en [3341 kB] Get:38 http://ftpmaster.internal precise-security/main Translation-en [73.6 kB] Get:39 http://ftpmaster.internal precise-security/multiverse Translation-en [587 B] Get:40 http://ftpmaster.internal precise-security/restricted Translation-en [978 B] Get:41 http://ftpmaster.internal precise-security/universe Translation-en [24.2 kB] Get:42 http://ftpmaster.internal precise-updates/main Translation-en [177 kB] Get:43 http://ftpmaster.internal precise-updates/multiverse Translation-en [1600 B] Get:44 http://ftpmaster.internal precise-updates/restricted Translation-en [1484 B] Get:45 http://ftpmaster.internal precise-updates/universe Translation-en [72.7 kB] Fetched 11.6 MB in 8s (1346 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files initscripts libapt-pkg4.12 libgcrypt11 libglib2.0-0 libgnutls26 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libsasl2-2 libssl1.0.0 libtasn1-3 libudev0 linux-libc-dev openssl perl perl-base perl-modules python2.7-minimal sysv-rc sysvinit-utils udev upstart 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After this operation, 37.9 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files perl perl-base perl-modules libapt-pkg4.12 apt libssl1.0.0 libglib2.0-0 libudev0 libgcrypt11 libtasn1-3 libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libsasl2-2 libldap-2.4-2 python2.7-minimal sysvinit-utils sysv-rc initscripts upstart udev apt-transport-https linux-libc-dev openssl Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise-updates/main base-files i386 6.5ubuntu6.2 [65.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main perl i386 5.14.2-6ubuntu2.1 [3685 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-base i386 5.14.2-6ubuntu2.1 [1472 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-modules all 5.14.2-6ubuntu2.1 [3396 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise-security/main libapt-pkg4.12 i386 0.8.16~exp12ubuntu10.2 [940 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-security/main apt i386 0.8.16~exp12ubuntu10.2 [1102 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-security/main libssl1.0.0 i386 1.0.1-4ubuntu5.3 [1006 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 i386 2.32.3-0ubuntu1 [1187 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 i386 175-0ubuntu9.1 [33.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main libgcrypt11 i386 1.5.0-3ubuntu0.1 [281 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 i386 2.10-1ubuntu1.1 [43.8 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 i386 2.12.14-5ubuntu3.1 [448 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 i386 1.10+dfsg~beta1-2ubuntu0.3 [77.4 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 i386 1.10+dfsg~beta1-2ubuntu0.3 [120 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 i386 1.10+dfsg~beta1-2ubuntu0.3 [366 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 i386 1.10+dfsg~beta1-2ubuntu0.3 [23.9 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 i386 2.1.25.dfsg1-3ubuntu0.1 [69.0 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 i386 2.4.28-1.1ubuntu4.1 [186 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-updates/main python2.7-minimal i386 2.7.3-0ubuntu3.1 [1693 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils i386 2.88dsf-13.10ubuntu11.1 [58.4 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise-updates/main sysv-rc all 2.88dsf-13.10ubuntu11.1 [44.6 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-updates/main initscripts i386 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart i386 1.5-0ubuntu7 [313 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-updates/main udev i386 175-0ubuntu9.1 [349 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-security/main apt-transport-https i386 0.8.16~exp12ubuntu10.2 [16.3 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev i386 3.2.0-29.46 [871 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-security/main openssl i386 1.0.1-4ubuntu5.3 [520 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.4 MB in 1s (14.1 MB/s) (Reading database ... 12281 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.2_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu6.2) ... 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 ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.1_i386.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.1_i386.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.1) ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-6ubuntu2 (using .../perl-modules_5.14.2-6ubuntu2.1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu10 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu10.2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12281 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu10.2) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: Total number processed: 2 gpg: unchanged: 2 (Reading database ... 12281 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.1-4ubuntu5.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12281 files and directories currently installed.) Preparing to replace libglib2.0-0 2.32.1-0ubuntu2 (using .../libglib2.0-0_2.32.3-0ubuntu1_i386.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libudev0 175-0ubuntu9 (using .../libudev0_175-0ubuntu9.1_i386.deb) ... Unpacking replacement libudev0 ... Preparing to replace libgcrypt11 1.5.0-3 (using .../libgcrypt11_1.5.0-3ubuntu0.1_i386.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libtasn1-3 2.10-1ubuntu1 (using .../libtasn1-3_2.10-1ubuntu1.1_i386.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.12.14-5ubuntu3 (using .../libgnutls26_2.12.14-5ubuntu3.1_i386.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.10+dfsg~beta1-2 (using .../libk5crypto3_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.10+dfsg~beta1-2 (using .../libgssapi-krb5-2_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.10+dfsg~beta1-2 (using .../libkrb5-3_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.10+dfsg~beta1-2 (using .../libkrb5support0_1.10+dfsg~beta1-2ubuntu0.3_i386.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.25.dfsg1-3 (using .../libsasl2-2_2.1.25.dfsg1-3ubuntu0.1_i386.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libldap-2.4-2 2.4.28-1.1ubuntu4 (using .../libldap-2.4-2_2.4.28-1.1ubuntu4.1_i386.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu3.1_i386.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.1) ... (Reading database ... 12281 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu11 (using .../sysv-rc_2.88dsf-13.10ubuntu11.1_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.88dsf-13.10ubuntu11 (using .../initscripts_2.88dsf-13.10ubuntu11.1_i386.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7_i386.deb) ... Unpacking replacement upstart ... Preparing to replace udev 175-0ubuntu9 (using .../udev_175-0ubuntu9.1_i386.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace apt-transport-https 0.8.16~exp12ubuntu10 (using .../apt-transport-https_0.8.16~exp12ubuntu10.2_i386.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace linux-libc-dev 3.2.0-23.36 (using .../linux-libc-dev_3.2.0-29.46_i386.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace openssl 1.0.1-4ubuntu3 (using .../openssl_1.0.1-4ubuntu5.3_i386.deb) ... Unpacking replacement openssl ... Setting up libglib2.0-0 (2.32.3-0ubuntu1) ... No schema files found: doing nothing. Setting up libudev0 (175-0ubuntu9.1) ... Setting up libgcrypt11 (1.5.0-3ubuntu0.1) ... Setting up libtasn1-3 (2.10-1ubuntu1.1) ... Setting up libgnutls26 (2.12.14-5ubuntu3.1) ... Setting up libkrb5support0 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libk5crypto3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libkrb5-3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libgssapi-krb5-2 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libsasl2-2 (2.1.25.dfsg1-3ubuntu0.1) ... Setting up libldap-2.4-2 (2.4.28-1.1ubuntu4.1) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu11.1) ... Setting up sysv-rc (2.88dsf-13.10ubuntu11.1) ... Setting up apt-transport-https (0.8.16~exp12ubuntu10.2) ... Setting up linux-libc-dev (3.2.0-29.46) ... Setting up openssl (1.0.1-4ubuntu5.3) ... Setting up perl-modules (5.14.2-6ubuntu2.1) ... Setting up upstart (1.5-0ubuntu7) ... Installing new version of config file /etc/logrotate.d/upstart ... Setting up udev (175-0ubuntu9.1) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up perl (5.14.2-6ubuntu2.1) ... Setting up initscripts (2.88dsf-13.10ubuntu11.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '2691b68befa9717391609bc22893696d18ce25cc', 'i386', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '-A', '--purpose=PPA', '--architecture=i386', '--comp=main', 'mrbayes_3.2.1+dfsg+repack-3ubuntu1.dsc'] Initiating build 2691b68befa9717391609bc22893696d18ce25cc with 2 jobs across 2 processor cores. Automatic build of mrbayes_3.2.1+dfsg+repack-3ubuntu1 on protactinium by sbuild/i386 1.170.5 Build started at 20120815-0207 ****************************************************************************** mrbayes_3.2.1+dfsg+repack-3ubuntu1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf (>= 2.65), automake (>= 1:1.11) Checking for already installed source dependencies... debhelper: missing libreadline-dev: missing mpi-default-dev: missing libhmsbeagle-dev: missing autoconf: missing automake: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper libreadline-dev mpi-default-dev libhmsbeagle-dev autoconf automake Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils dh-apparmor file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libhmsbeagle1 libibverbs-dev libibverbs1 libmagic1 libnuma1 libopenmpi-dev libopenmpi1.3 libpipeline1 libreadline6-dev libtinfo-dev libtorque2 libunistring0 libxml2 m4 man-db openmpi-common po-debconf Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper dh-apparmor file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libhmsbeagle-dev libhmsbeagle1 libibverbs-dev libibverbs1 libmagic1 libnuma1 libopenmpi-dev libopenmpi1.3 libpipeline1 libreadline-dev libreadline6-dev libtinfo-dev libtorque2 libunistring0 libxml2 m4 man-db mpi-default-dev openmpi-common po-debconf 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 11.8 MB of archives. After this operation, 39.4 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 libmagic1 file bsdmainutils gettext-base groff-base man-db m4 autoconf autotools-dev automake html2text gettext intltool-debian po-debconf dh-apparmor debhelper libnuma1 libtinfo-dev libreadline6-dev libreadline-dev libtorque2 openmpi-common libhmsbeagle1 libhmsbeagle-dev libibverbs1 libibverbs-dev libopenmpi1.3 libopenmpi-dev mpi-default-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 i386 1.2.1-1 [26.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 i386 2.7.8.dfsg-5.1ubuntu4.1 [662 kB] Get:3 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main libhmsbeagle1 i386 0.1052-2 [106 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 i386 0.6.5-1 [99.7 kB] Get:5 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main libhmsbeagle-dev i386 0.1052-2 [125 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 i386 0.9.3-5 [432 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 i386 0.18.1.1-5ubuntu3 [118 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 i386 5.09-2 [219 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main file i386 5.09-2 [19.4 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils i386 8.2.3ubuntu1 [194 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main gettext-base i386 0.18.1.1-5ubuntu3 [58.2 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main groff-base i386 1.21-7 [1024 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main man-db i386 2.6.1-2 [747 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main m4 i386 1.4.16-2ubuntu1 [195 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main autoconf all 2.68-1ubuntu2 [560 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main autotools-dev all 20120210.1ubuntu1 [42.4 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main automake all 1:1.11.3-1ubuntu2 [571 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main html2text i386 1.3.2a-15 [101 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main gettext i386 0.18.1.1-5ubuntu3 [1122 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-security/main dh-apparmor all 2.7.102-0ubuntu3.1 [9546 B] Get:23 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libnuma1 i386 2.0.8~rc3-1 [23.5 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libtinfo-dev i386 5.9-4 [93.5 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main libreadline6-dev i386 6.2-8 [249 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libreadline-dev i386 6.2-8 [932 B] Get:28 http://ftpmaster.internal/ubuntu/ precise/universe libtorque2 i386 2.4.16+dfsg-1build1 [87.4 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/universe openmpi-common all 1.4.3-2.1ubuntu3 [84.4 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libibverbs1 i386 1.1.5-1ubuntu1 [28.5 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libibverbs-dev i386 1.1.5-1ubuntu1 [74.4 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi1.3 i386 1.4.3-2.1ubuntu3 [1290 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi-dev i386 1.4.3-2.1ubuntu3 [2623 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/universe mpi-default-dev i386 1.0.1 [3642 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.8 MB in 1s (8926 kB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12283 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_i386.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.1_i386.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_i386.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_i386.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_i386.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_i386.deb) ... 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Selecting previously unselected package libreadline-dev. Unpacking libreadline-dev (from .../libreadline-dev_6.2-8_i386.deb) ... Selecting previously unselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.16+dfsg-1build1_i386.deb) ... Selecting previously unselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.4.3-2.1ubuntu3_all.deb) ... Selecting previously unselected package libhmsbeagle1. Unpacking libhmsbeagle1 (from .../libhmsbeagle1_0.1052-2_i386.deb) ... Selecting previously unselected package libhmsbeagle-dev. Unpacking libhmsbeagle-dev (from .../libhmsbeagle-dev_0.1052-2_i386.deb) ... Selecting previously unselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.5-1ubuntu1_i386.deb) ... Selecting previously unselected package libibverbs-dev. Unpacking libibverbs-dev (from .../libibverbs-dev_1.1.5-1ubuntu1_i386.deb) ... Selecting previously unselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.3-2.1ubuntu3_i386.deb) ... Selecting previously unselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.3-2.1ubuntu3_i386.deb) ... Selecting previously unselected package mpi-default-dev. Unpacking mpi-default-dev (from .../mpi-default-dev_1.0.1_i386.deb) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.1) ... Setting up libcroco3 (0.6.5-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up bsdmainutils (8.2.3ubuntu1) ... 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 gettext-base (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up m4 (1.4.16-2ubuntu1) ... Setting up autoconf (2.68-1ubuntu2) ... Setting up autotools-dev (20120210.1ubuntu1) ... Setting up automake (1:1.11.3-1ubuntu2) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3.1) ... Setting up debhelper (9.20120115ubuntu3) ... Setting up libnuma1 (2.0.8~rc3-1) ... Setting up libtinfo-dev (5.9-4) ... Setting up libreadline6-dev (6.2-8) ... Setting up libreadline-dev (6.2-8) ... Setting up libtorque2 (2.4.16+dfsg-1build1) ... Setting up openmpi-common (1.4.3-2.1ubuntu3) ... Setting up libhmsbeagle1 (0.1052-2) ... Setting up libhmsbeagle-dev (0.1052-2) ... Setting up libibverbs1 (1.1.5-1ubuntu1) ... Setting up libibverbs-dev (1.1.5-1ubuntu1) ... Setting up libopenmpi1.3 (1.4.3-2.1ubuntu3) ... Setting up libopenmpi-dev (1.4.3-2.1ubuntu3) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode. Setting up mpi-default-dev (1.0.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu10 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu7 gcc-4.6_4.6.3-1ubuntu5 g++-4.6_4.6.3-1ubuntu5 binutils_2.22-6ubuntu1 libstdc++6-4.6-dev_4.6.3-1ubuntu5 libstdc++6_4.6.3-1ubuntu5 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Fri Aug 10 15:27:48 2012 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.1+dfsg+repack-3ubuntu1.dsc dpkg-source: info: extracting mrbayes in mrbayes-3.2.1+dfsg+repack dpkg-source: info: unpacking mrbayes_3.2.1+dfsg+repack.orig.tar.gz dpkg-source: info: unpacking mrbayes_3.2.1+dfsg+repack-3ubuntu1.debian.tar.gz dpkg-source: info: applying as-needed.patch dpkg-buildpackage: source package mrbayes dpkg-buildpackage: source version 3.2.1+dfsg+repack-3ubuntu1 dpkg-source --before-build mrbayes-3.2.1+dfsg+repack dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --sourcedirectory=src dh_testdir -O--sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' ( cd src ; /usr/bin/make -f Makefile.in distclean ) make[2]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' rm -f *.o *~ mb rm -f Makefile config.log config.status config.cache config.h make[2]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' rm -f src/configure rm -f mb mb-mpi src/mb make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_clean -O--sourcedirectory=src debian/rules build dh build --sourcedirectory=src dh_testdir -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' #Configure for MPI at first ( cd src ; autoconf ) dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the default MrBayes flags will be overridden. To ensure optimal performance, please check that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS variable in your shell in order to use the default MrBayes compiler options. 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 how to run the C preprocessor... gcc -E 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 exp in -lm... yes checking for a BSD-compatible install... /usr/bin/install -c checking for mpicc... yes checking for SSE support... no checking for /usr/include/libhmsbeagle-1... yes checking for /usr/lib... yes checking for readline in -lreadline... yes checking for rl_completion_matches function... yes checking for 32 or 64 bits cpu... 32 configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make[2]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o command.o command.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbmath.o mbmath.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o model.o model.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o plot.o plot.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sump.o sump.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumt.o sumt.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o tree.o tree.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o best.o best.c mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro mb.c bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o tree.o utils.o mbbeagle.o best.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm -o mb make[2]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' rm -f *.o *~ mb make[2]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the default MrBayes flags will be overridden. To ensure optimal performance, please check that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS variable in your shell in order to use the default MrBayes compiler options. 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 how to run the C preprocessor... gcc -E 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 exp in -lm... yes checking for a BSD-compatible install... /usr/bin/install -c checking for SSE support... no checking for /usr/include/libhmsbeagle-1... yes checking for /usr/lib... yes checking for readline in -lreadline... yes checking for rl_completion_matches function... yes checking for 32 or 64 bits cpu... 32 configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking LIBS="-Wl,--as-needed" dh_auto_build make[2]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o command.o command.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbmath.o mbmath.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o model.o model.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o plot.o plot.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sump.o sump.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumt.o sumt.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o tree.o tree.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o best.o best.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro mb.c bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o tree.o utils.o mbbeagle.o best.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm -o mb make[2]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack/src' mv src/mb . make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_auto_test -O--sourcedirectory=src /usr/bin/fakeroot debian/rules binary dh binary --sourcedirectory=src dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_installdirs -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installcatalogs -O--sourcedirectory=src dh_installcron -O--sourcedirectory=src dh_installdebconf -O--sourcedirectory=src dh_installemacsen -O--sourcedirectory=src dh_installifupdown -O--sourcedirectory=src dh_installinfo -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_installmenu -O--sourcedirectory=src dh_installmime -O--sourcedirectory=src dh_installmodules -O--sourcedirectory=src dh_installlogcheck -O--sourcedirectory=src dh_installlogrotate -O--sourcedirectory=src dh_installpam -O--sourcedirectory=src dh_installppp -O--sourcedirectory=src dh_installudev -O--sourcedirectory=src dh_installwm -O--sourcedirectory=src dh_installxfonts -O--sourcedirectory=src dh_installgsettings -O--sourcedirectory=src dh_bugfiles -O--sourcedirectory=src dh_ucf -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_gconf -O--sourcedirectory=src dh_icons -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_usrlocal -O--sourcedirectory=src dh_link -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_compress --exclude=.pdf make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_fixperms -O--sourcedirectory=src debian/rules override_dh_strip make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_strip --dbg-package=mrbayes-dbg dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi" were not uselessly linked against it (they use none of its symbols). dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src debian/rules override_dh_builddeb make[1]: Entering directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dh_builddeb -- -Z xz INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `mrbayes' in `../mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb'. INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `mrbayes-mpi' in `../mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb'. INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `mrbayes-dbg' in `../mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb'. INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `mrbayes-doc' in `../mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb'. make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dpkg-genchanges -b -mUbuntu Build Daemon >../mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build mrbayes-3.2.1+dfsg+repack dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120815-0212 chroot-autobuild/build/buildd/mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb: new debian package, version 2.0. size 475062 bytes: control archive= 870 bytes. 886 bytes, 19 lines control 318 bytes, 5 lines md5sums Package: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 1442 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.7), libhmsbeagle1, libreadline6 (>= 6.0) Suggests: mrbayes-doc Section: science Priority: optional Homepage: http://mrbayes.csit.fsu.edu/ Description: Bayesian Inference of Phylogeny Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. chroot-autobuild/build/buildd/mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb: new debian package, version 2.0. size 504892 bytes: control archive= 980 bytes. 1042 bytes, 22 lines control 399 bytes, 6 lines md5sums Package: mrbayes-mpi Source: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 1526 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.7), libhmsbeagle1, libopenmpi1.3, libreadline6 (>= 6.0), mpi-default-bin Suggests: mpi-default, mrbayes-doc Section: science Priority: optional Homepage: http://mrbayes.csit.fsu.edu/ Description: Bayesian Inference of Phylogeny - mpi version Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . This package offers a binary compiled for parallel computation with MPI. chroot-autobuild/build/buildd/mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb: new debian package, version 2.0. size 1193498 bytes: control archive= 1018 bytes. 1321 bytes, 24 lines control 362 bytes, 4 lines md5sums Package: mrbayes-dbg Source: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 1290 Pre-Depends: dpkg (>= 1.15.6~) Depends: mrbayes (= 3.2.1+dfsg+repack-3ubuntu1) | mrbayes-mpi (= 3.2.1+dfsg+repack-3ubuntu1) Conflicts: mrbayes (>> 3.2.1+dfsg+repack-3ubuntu1), mrbayes (<< 3.2.1+dfsg+repack-3ubuntu1), mrbayes-mpi (>> 3.2.1+dfsg+repack-3ubuntu1), mrbayes-mpi (<< 3.2.1+dfsg+repack-3ubuntu1) Section: debug Priority: extra Homepage: http://mrbayes.csit.fsu.edu/ Description: Bayesian Inference of Phylogeny - debug symbols Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . The package provides the debug symbols that are otherwise stripped from the binaries to reduce the footprint of the package. This package can be installed to help debugging of problems when running mrbayes. chroot-autobuild/build/buildd/mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb: new debian package, version 2.0. size 1321620 bytes: control archive= 843 bytes. 891 bytes, 21 lines control 303 bytes, 4 lines md5sums Package: mrbayes-doc Source: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 1413 Pre-Depends: dpkg (>= 1.15.6~) Enhances: mrbayes Section: doc Priority: extra Homepage: http://mrbayes.csit.fsu.edu/ Description: Bayesian Inference of Phylogeny - manual Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. . This package provides the manual for MrBayes. chroot-autobuild/build/buildd/mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb' contains ununderstood data member data.tar.xz , giving up chroot-autobuild/build/buildd/mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb' contains ununderstood data member data.tar.xz , giving up chroot-autobuild/build/buildd/mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb' contains ununderstood data member data.tar.xz , giving up chroot-autobuild/build/buildd/mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb' contains ununderstood data member data.tar.xz , giving up mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.changes: Format: 1.8 Date: Fri, 10 Aug 2012 15:58:14 +0100 Source: mrbayes Binary: mrbayes mrbayes-mpi mrbayes-dbg mrbayes-doc Architecture: i386 all Version: 3.2.1+dfsg+repack-3ubuntu1 Distribution: precise Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Tim Booth Description: mrbayes - Bayesian Inference of Phylogeny mrbayes-dbg - Bayesian Inference of Phylogeny - debug symbols mrbayes-doc - Bayesian Inference of Phylogeny - manual mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version Changes: mrbayes (3.2.1+dfsg+repack-3ubuntu1) precise; urgency=low . * Rebuild for Ubuntu. Fix Lintian warning about xz Checksums-Sha1: 66b719278c79ee9b06150ed681ea44627ec7a3ad 475062 mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb 89d6a88ec9222d4aac3fbf08bb0e25ad72471cda 504892 mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb f1c80ef21c9d894f0e79d8c9d9177b96aab59421 1193498 mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb 21b49802a026becbeef5e4b4275823bdb8620733 1321620 mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb Checksums-Sha256: 7e6080b80b827b36cd5cc4e3a73f033419f7229b029b80691d3ee3d29b4da2a1 475062 mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb f85a3f01c314a3301ef433f11002f52abc156ef160000219c00507001fcfa32e 504892 mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb 55624eac25197c193aa7eee514072f8bc08dd7a3132bf04c8aa96df1afd311a5 1193498 mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb bb74218f2887dcfb369c4f8dc62804f7aa4fb57751701822875b3d98450e958f 1321620 mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb Files: 4aac85689de9bd671e97fb0fe89dae54 475062 science optional mrbayes_3.2.1+dfsg+repack-3ubuntu1_i386.deb ad9405965f3d988b826a12d82a7a00fa 504892 science optional mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_i386.deb 60da6a3e4892bce9012b18ec7dc82dd0 1193498 debug extra mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_i386.deb ab620a5d97ee019698c2d3bb69531ec8 1321620 doc extra mrbayes-doc_3.2.1+dfsg+repack-3ubuntu1_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120815-0212 Build needed 00:02:21, 26936k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '2691b68befa9717391609bc22893696d18ce25cc'] Scanning for processes to kill in build /home/buildd/build-2691b68befa9717391609bc22893696d18ce25cc/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '2691b68befa9717391609bc22893696d18ce25cc'] Unmounting chroot for build 2691b68befa9717391609bc22893696d18ce25cc... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '2691b68befa9717391609bc22893696d18ce25cc'] Removing build 2691b68befa9717391609bc22893696d18ce25cc