RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '8fd41bff77fcdc79132b77961a6d803f9a2360fb', '/home/buildd/filecache-default/c021ff3d3373fb2201b3008c0ece6808393ff246'] Uncompressing the tarball... Synching the system clock with the buildd NTP service... 17 Oct 00:12:53 ntpdate[3400]: step time server 10.211.37.1 offset -5461306.024279 sec Unpacking chroot for build 8fd41bff77fcdc79132b77961a6d803f9a2360fb RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '8fd41bff77fcdc79132b77961a6d803f9a2360fb'] Mounting chroot for build 8fd41bff77fcdc79132b77961a6d803f9a2360fb RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '8fd41bff77fcdc79132b77961a6d803f9a2360fb', '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-8fd41bff77fcdc79132b77961a6d803f9a2360fb RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '8fd41bff77fcdc79132b77961a6d803f9a2360fb', 'amd64'] Updating debian chroot for build 8fd41bff77fcdc79132b77961a6d803f9a2360fb 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] Get:5 http://ftpmaster.internal precise-security Release [49.6 kB] Get:6 http://ftpmaster.internal precise-updates Release [49.6 kB] Get:7 http://ftpmaster.internal precise/main amd64 Packages [1273 kB] Get:8 http://ftpmaster.internal precise/restricted amd64 Packages [8452 B] Get:9 http://ftpmaster.internal precise/universe amd64 Packages [4786 kB] Get:10 http://ftpmaster.internal precise/multiverse amd64 Packages [119 kB] Ign http://ppa.launchpad.net precise InRelease Get:11 http://ftpmaster.internal precise/main TranslationIndex [3706 B] Get:12 http://ftpmaster.internal precise/multiverse TranslationIndex [2676 B] Get:13 http://ftpmaster.internal precise/restricted TranslationIndex [2596 B] Get:14 http://ftpmaster.internal precise/universe TranslationIndex [2922 B] Get:15 http://ftpmaster.internal precise-security/main amd64 Packages [155 kB] Get:16 http://ftpmaster.internal precise-security/restricted amd64 Packages [3969 B] Get:17 http://ftpmaster.internal precise-security/universe amd64 Packages [38.7 kB] Get:18 http://ftpmaster.internal precise-security/multiverse amd64 Packages [1155 B] Get:19 http://ftpmaster.internal precise-security/main TranslationIndex [73 B] Get:20 http://ftpmaster.internal precise-security/multiverse TranslationIndex [71 B] Get:21 http://ftpmaster.internal precise-security/restricted TranslationIndex [71 B] Get:22 http://ftpmaster.internal precise-security/universe TranslationIndex [73 B] Get:23 http://ftpmaster.internal precise-updates/main amd64 Packages [366 kB] Get:24 http://ftpmaster.internal precise-updates/restricted amd64 Packages [6755 B] Get:25 http://ftpmaster.internal precise-updates/universe amd64 Packages [121 kB] Get:26 http://ftpmaster.internal precise-updates/multiverse amd64 Packages [2365 B] Get:27 http://ftpmaster.internal precise-updates/main TranslationIndex [3564 B] Get:28 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [2605 B] Get:29 http://ftpmaster.internal precise-updates/restricted TranslationIndex [2461 B] Get:30 http://ftpmaster.internal precise-updates/universe TranslationIndex [2850 B] Get:31 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:32 http://ppa.launchpad.net precise Release.gpg [316 B] Get:33 http://ppa.launchpad.net precise Release [11.9 kB] Ign http://ppa.launchpad.net precise Release Get:34 http://ftpmaster.internal precise/multiverse Translation-en [93.4 kB] Get:35 http://ftpmaster.internal precise/restricted Translation-en [2395 B] Get:36 http://ftpmaster.internal precise/universe Translation-en [3341 kB] Get:37 http://ppa.launchpad.net precise/main amd64 Packages [4728 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Ign http://ppa.launchpad.net precise/main Translation-en 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 4s (2698 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 19.2 MB of archives. After this operation, 35.8 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 amd64 6.5ubuntu6.2 [69.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main perl amd64 5.14.2-6ubuntu2.1 [4416 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-base amd64 5.14.2-6ubuntu2.1 [1498 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 amd64 0.8.16~exp12ubuntu10.2 [932 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-security/main apt amd64 0.8.16~exp12ubuntu10.2 [1092 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-security/main libssl1.0.0 amd64 1.0.1-4ubuntu5.3 [1011 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 amd64 2.32.3-0ubuntu1 [1199 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 amd64 175-0ubuntu9.1 [30.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main libgcrypt11 amd64 1.5.0-3ubuntu0.1 [280 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 amd64 2.10-1ubuntu1.1 [43.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 amd64 2.12.14-5ubuntu3.1 [459 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [80.1 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 amd64 1.10+dfsg~beta1-2ubuntu0.3 [118 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [355 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 amd64 1.10+dfsg~beta1-2ubuntu0.3 [23.8 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 amd64 2.1.25.dfsg1-3ubuntu0.1 [69.1 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 amd64 2.4.28-1.1ubuntu4.1 [186 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-updates/main python2.7-minimal amd64 2.7.3-0ubuntu3.1 [1741 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils amd64 2.88dsf-13.10ubuntu11.1 [60.2 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 amd64 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart amd64 1.5-0ubuntu7 [311 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-updates/main udev amd64 175-0ubuntu9.1 [323 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-security/main apt-transport-https amd64 0.8.16~exp12ubuntu10.2 [16.3 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev amd64 3.2.0-29.46 [871 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-security/main openssl amd64 1.0.1-4ubuntu5.3 [523 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.2 MB in 0s (24.9 MB/s) (Reading database ... 12243 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.2_amd64.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 ... 12243 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.1) ... (Reading database ... 12243 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_amd64.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 ... 12243 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.2_amd64.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 ... 12243 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.3_amd64.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 ... 12243 files and directories currently installed.) Preparing to replace libglib2.0-0 2.32.1-0ubuntu2 (using .../libglib2.0-0_2.32.3-0ubuntu1_amd64.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libudev0 175-0ubuntu9 (using .../libudev0_175-0ubuntu9.1_amd64.deb) ... Unpacking replacement libudev0 ... Preparing to replace libgcrypt11 1.5.0-3 (using .../libgcrypt11_1.5.0-3ubuntu0.1_amd64.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libtasn1-3 2.10-1ubuntu1 (using .../libtasn1-3_2.10-1ubuntu1.1_amd64.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.12.14-5ubuntu3 (using .../libgnutls26_2.12.14-5ubuntu3.1_amd64.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.10+dfsg~beta1-2 (using .../libk5crypto3_1.10+dfsg~beta1-2ubuntu0.3_amd64.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_amd64.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_amd64.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.10+dfsg~beta1-2 (using .../libkrb5support0_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.25.dfsg1-3 (using .../libsasl2-2_2.1.25.dfsg1-3ubuntu0.1_amd64.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_amd64.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_amd64.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.1) ... (Reading database ... 12243 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_amd64.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_amd64.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7_amd64.deb) ... Unpacking replacement upstart ... Preparing to replace udev 175-0ubuntu9 (using .../udev_175-0ubuntu9.1_amd64.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_amd64.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_amd64.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace openssl 1.0.1-4ubuntu3 (using .../openssl_1.0.1-4ubuntu5.3_amd64.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', '8fd41bff77fcdc79132b77961a6d803f9a2360fb', 'amd64', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=PPA', '--architecture=amd64', '--comp=main', 'mrbayes_3.2.1+dfsg+repack-3ubuntu1.dsc'] Initiating build 8fd41bff77fcdc79132b77961a6d803f9a2360fb with 2 processor cores. Automatic build of mrbayes_3.2.1+dfsg+repack-3ubuntu1 on litembilla by sbuild/amd64 1.170.5 Build started at 20120814-1914 ****************************************************************************** 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 12.2 MB of archives. After this operation, 42.9 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 amd64 1.2.1-1 [26.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 amd64 2.7.8.dfsg-5.1ubuntu4.1 [673 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 amd64 0.6.5-1 [99.3 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 amd64 0.9.3-5 [427 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 amd64 0.18.1.1-5ubuntu3 [120 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 amd64 5.09-2 [217 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main file amd64 5.09-2 [19.7 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils amd64 8.2.3ubuntu1 [200 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main gettext-base amd64 0.18.1.1-5ubuntu3 [80.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main groff-base amd64 1.21-7 [1046 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main man-db amd64 2.6.1-2 [756 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main m4 amd64 1.4.16-2ubuntu1 [200 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main autoconf all 2.68-1ubuntu2 [560 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main autotools-dev all 20120210.1ubuntu1 [42.4 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main automake all 1:1.11.3-1ubuntu2 [571 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main html2text amd64 1.3.2a-15 [104 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main gettext amd64 0.18.1.1-5ubuntu3 [1188 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-security/main dh-apparmor all 2.7.102-0ubuntu3.1 [9546 B] Get:21 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main libnuma1 amd64 2.0.8~rc3-1 [23.1 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main libtinfo-dev amd64 5.9-4 [103 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libreadline6-dev amd64 6.2-8 [264 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libreadline-dev amd64 6.2-8 [932 B] Get:26 http://ftpmaster.internal/ubuntu/ precise/universe libtorque2 amd64 2.4.16+dfsg-1build1 [91.6 kB] Get:27 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main libhmsbeagle1 amd64 0.1052-2 [110 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/universe openmpi-common all 1.4.3-2.1ubuntu3 [84.4 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libibverbs1 amd64 1.1.5-1ubuntu1 [27.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libibverbs-dev amd64 1.1.5-1ubuntu1 [76.1 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi1.3 amd64 1.4.3-2.1ubuntu3 [1350 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/universe libopenmpi-dev amd64 1.4.3-2.1ubuntu3 [2718 kB] Get:33 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main libhmsbeagle-dev amd64 0.1052-2 [126 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/universe mpi-default-dev amd64 1.0.1 [3648 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.2 MB in 0s (26.7 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12245 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_amd64.deb) ... 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Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.3-2.1ubuntu3_amd64.deb) ... Selecting previously unselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.3-2.1ubuntu3_amd64.deb) ... Selecting previously unselected package mpi-default-dev. Unpacking mpi-default-dev (from .../mpi-default-dev_1.0.1_amd64.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 amd64 /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... yes 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... 64 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... yes 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... 64 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-arch dh binary-arch --sourcedirectory=src dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_installdirs -a -O--sourcedirectory=src dh_auto_install -a -O--sourcedirectory=src dh_install -a -O--sourcedirectory=src dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src dh_installexamples -a -O--sourcedirectory=src dh_installman -a -O--sourcedirectory=src dh_installcatalogs -a -O--sourcedirectory=src dh_installcron -a -O--sourcedirectory=src dh_installdebconf -a -O--sourcedirectory=src dh_installemacsen -a -O--sourcedirectory=src dh_installifupdown -a -O--sourcedirectory=src dh_installinfo -a -O--sourcedirectory=src dh_installinit -a -O--sourcedirectory=src dh_installmenu -a -O--sourcedirectory=src dh_installmime -a -O--sourcedirectory=src dh_installmodules -a -O--sourcedirectory=src dh_installlogcheck -a -O--sourcedirectory=src dh_installlogrotate -a -O--sourcedirectory=src dh_installpam -a -O--sourcedirectory=src dh_installppp -a -O--sourcedirectory=src dh_installudev -a -O--sourcedirectory=src dh_installwm -a -O--sourcedirectory=src dh_installxfonts -a -O--sourcedirectory=src dh_installgsettings -a -O--sourcedirectory=src dh_bugfiles -a -O--sourcedirectory=src dh_ucf -a -O--sourcedirectory=src dh_lintian -a -O--sourcedirectory=src dh_gconf -a -O--sourcedirectory=src dh_icons -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_usrlocal -a -O--sourcedirectory=src dh_link -a -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 -a -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 -a -O--sourcedirectory=src dh_shlibdeps -a -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 -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -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_amd64.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_amd64.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_amd64.deb'. make[1]: Leaving directory `/build/buildd/mrbayes-3.2.1+dfsg+repack' dpkg-genchanges -B -mUbuntu/i386 Build Daemon >../mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build mrbayes-3.2.1+dfsg+repack dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120814-1917 chroot-autobuild/build/buildd/mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.deb: new debian package, version 2.0. size 534104 bytes: control archive= 868 bytes. 888 bytes, 19 lines control 318 bytes, 5 lines md5sums Package: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1508 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.14), 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_amd64.deb: new debian package, version 2.0. size 565288 bytes: control archive= 987 bytes. 1044 bytes, 22 lines control 399 bytes, 6 lines md5sums Package: mrbayes-mpi Source: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1597 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.14), 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_amd64.deb: new debian package, version 2.0. size 1331376 bytes: control archive= 1024 bytes. 1322 bytes, 24 lines control 362 bytes, 4 lines md5sums Package: mrbayes-dbg Source: mrbayes Version: 3.2.1+dfsg+repack-3ubuntu1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1458 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_3.2.1+dfsg+repack-3ubuntu1_amd64.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.deb' contains ununderstood data member data.tar.xz , giving up chroot-autobuild/build/buildd/mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_amd64.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_amd64.deb' contains ununderstood data member data.tar.xz , giving up chroot-autobuild/build/buildd/mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_amd64.deb: dpkg-deb: file `chroot-autobuild/build/buildd/mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_amd64.deb' contains ununderstood data member data.tar.xz , giving up mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.changes: Format: 1.8 Date: Fri, 10 Aug 2012 15:58:14 +0100 Source: mrbayes Binary: mrbayes mrbayes-mpi mrbayes-dbg mrbayes-doc Architecture: amd64 Version: 3.2.1+dfsg+repack-3ubuntu1 Distribution: precise Urgency: low Maintainer: Ubuntu/i386 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: 767de597f5f66c299f5b1d5637fd9ea667de6c5f 534104 mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.deb 9a113b1e30dffd4514dc6bc00061afb6681086a0 565288 mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_amd64.deb a4b06f4e42f65781f77d57c2f119ff11f9b59a7f 1331376 mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_amd64.deb Checksums-Sha256: f20cca8bd46405c12d5859a2171f81a72bd0c9779c948d870dae41b434a1427b 534104 mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.deb 89220620027c783c0193f776c478d9d06a15ae30addd51191ec4510c9521886a 565288 mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_amd64.deb 997431bd5e153bb44786664195f28a37af00f1bf04504141505a7cc38d0ab3e0 1331376 mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_amd64.deb Files: f94c81f27ad75d457fbfdd8342ddd4ed 534104 science optional mrbayes_3.2.1+dfsg+repack-3ubuntu1_amd64.deb f86a8a93c4a90d4c11374df80439910b 565288 science optional mrbayes-mpi_3.2.1+dfsg+repack-3ubuntu1_amd64.deb 03cbaaa46093d7d950d1e039815de94e 1331376 debug extra mrbayes-dbg_3.2.1+dfsg+repack-3ubuntu1_amd64.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/mrbayes-3.2.1+dfsg+repack ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base libibverbs-dev libtorque2 m4 gettext file libibverbs1 autotools-dev po-debconf libopenmpi-dev libcroco3 libhmsbeagle1 libopenmpi1.3 libnuma1 libxml2 automake libgettextpo0 man-db intltool-debian libreadline-dev dh-apparmor html2text libreadline6-dev gettext-base debhelper mpi-default-dev libunistring0 libtinfo-dev libmagic1 libpipeline1 libhmsbeagle-dev bsdmainutils openmpi-common autoconf (Reading database ... 14740 files and directories currently installed.) Removing automake ... Removing libreadline-dev ... Removing libreadline6-dev ... Removing debhelper ... Removing mpi-default-dev ... Removing libtinfo-dev ... Removing libhmsbeagle-dev ... Removing autoconf ... Purging configuration files for autoconf ... Removing m4 ... Removing file ... Removing autotools-dev ... Removing po-debconf ... Removing libopenmpi-dev ... Removing libhmsbeagle1 ... Purging configuration files for libhmsbeagle1 ... Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libnuma1 ... Purging configuration files for libnuma1 ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing dh-apparmor ... Removing html2text ... Purging configuration files for html2text ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing openmpi-common ... Removing groff-base ... Purging configuration files for groff-base ... Removing libibverbs-dev ... Removing libtorque2 ... Purging configuration files for libtorque2 ... Removing gettext ... Removing libibverbs1 ... Purging configuration files for libibverbs1 ... Removing libgettextpo0 ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20120814-1917 Build needed 00:01:51, 28548k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '8fd41bff77fcdc79132b77961a6d803f9a2360fb'] Scanning for processes to kill in build /home/buildd/build-8fd41bff77fcdc79132b77961a6d803f9a2360fb/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '8fd41bff77fcdc79132b77961a6d803f9a2360fb'] Unmounting chroot for build 8fd41bff77fcdc79132b77961a6d803f9a2360fb... none /home/buildd/build-8fd41bff77fcdc79132b77961a6d803f9a2360fb/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-8fd41bff77fcdc79132b77961a6d803f9a2360fb/chroot-autobuild/dev/pts devpts rw,relatime 0 0 none /home/buildd/build-8fd41bff77fcdc79132b77961a6d803f9a2360fb/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-8fd41bff77fcdc79132b77961a6d803f9a2360fb/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '8fd41bff77fcdc79132b77961a6d803f9a2360fb'] Removing build 8fd41bff77fcdc79132b77961a6d803f9a2360fb