RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kishi06 3.2.0-68-highbank #102-Ubuntu SMP PREEMPT Tue Aug 12 22:53:28 UTC 2014 armv7l Buildd toolchain package versions: launchpad-buildd_125 python-lpbuildd_125 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.5. Syncing the system clock with the buildd NTP service... 25 Oct 18:38:54 ntpdate[25409]: adjust time server 10.211.37.1 offset 0.000174 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6505003', '/home/buildd/filecache-default/d07e8cc4ecf4426b85f8dac93ffd1d24d96a58d8'] Unpacking chroot for build PACKAGEBUILD-6505003 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6505003'] Mounting chroot for build PACKAGEBUILD-6505003 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6505003', 'deb http://ftpmaster.internal/ubuntu vivid main universe', 'deb http://ftpmaster.internal/ubuntu vivid-security main universe', 'deb http://ftpmaster.internal/ubuntu vivid-updates main universe', 'deb http://ftpmaster.internal/ubuntu vivid-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-6505003 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6505003', 'armhf'] Updating debian chroot for build PACKAGEBUILD-6505003 Ign http://archive-team.internal vivid InRelease Ign http://ftpmaster.internal vivid InRelease Ign http://archive-team.internal vivid Release.gpg Ign http://ftpmaster.internal vivid-security InRelease Get:1 http://archive-team.internal vivid Release [728 B] Ign http://ftpmaster.internal vivid-updates InRelease Ign http://ftpmaster.internal vivid-proposed InRelease Get:2 http://ftpmaster.internal vivid Release.gpg [933 B] Get:3 http://ftpmaster.internal vivid-security Release.gpg [933 B] Get:4 http://ftpmaster.internal vivid-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal vivid-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal vivid Release [112 kB] Get:7 http://archive-team.internal vivid/main armhf Packages Get:8 http://ftpmaster.internal vivid-security Release [59.7 kB] Get:9 http://ftpmaster.internal vivid-updates Release [59.7 kB] Ign http://archive-team.internal vivid/main Translation-en Get:10 http://ftpmaster.internal vivid-proposed Release [59.7 kB] Get:11 http://ftpmaster.internal vivid/main armhf Packages [1302 kB] Get:12 http://ftpmaster.internal vivid/universe armhf Packages [6053 kB] Get:13 http://ftpmaster.internal vivid/main Translation-en [769 kB] Get:14 http://ftpmaster.internal vivid/universe Translation-en [4279 kB] Get:15 http://ftpmaster.internal vivid-security/main armhf Packages [14 B] Get:16 http://ftpmaster.internal vivid-security/universe armhf Packages [14 B] Get:17 http://ftpmaster.internal vivid-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal vivid-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal vivid-updates/main armhf Packages [14 B] Get:20 http://ftpmaster.internal vivid-updates/universe armhf Packages [14 B] Get:21 http://ftpmaster.internal vivid-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal vivid-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal vivid-proposed/main armhf Packages [49.5 kB] Get:24 http://ftpmaster.internal vivid-proposed/universe armhf Packages [418 kB] Get:25 http://ftpmaster.internal vivid-proposed/main Translation-en [52.6 kB] Get:26 http://ftpmaster.internal vivid-proposed/universe Translation-en [291 kB] Fetched 13.5 MB in 17s (789 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils ca-certificates cpp-4.9 g++-4.9 gcc-4.9 gcc-4.9-base grep libacl1 libasan1 libatomic1 libdb5.3 libdrm2 libgcc-4.9-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libp11-kit0 libplymouth4 libsasl2-2 libsasl2-modules-db libselinux1 libsqlite3-0 libstdc++-4.9-dev libstdc++6 libsystemd-journal0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 patch perl perl-base perl-modules plymouth tzdata udev 42 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 31.4 MB of archives. After this operation, 193 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main base-files armhf 7.2ubuntu8 [66.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main grep armhf 2.20-4 [135 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl armhf 5.20.1-2 [2081 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-base armhf 5.20.1-2 [1107 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-modules all 5.20.1-2 [2531 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libdb5.3 armhf 5.3.28-6 [594 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libubsan0 armhf 4.9.1-19ubuntu1 [72.1 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9-base armhf 4.9.1-19ubuntu1 [15.9 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++6 armhf 4.9.1-19ubuntu1 [249 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgomp1 armhf 4.9.1-19ubuntu1 [36.9 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libatomic1 armhf 4.9.1-19ubuntu1 [6364 B] Get:12 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libasan1 armhf 4.9.1-19ubuntu1 [174 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc-4.9-dev armhf 4.9.1-19ubuntu1 [369 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid-proposed/main cpp-4.9 armhf 4.9.1-19ubuntu1 [4293 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid-proposed/main binutils armhf 2.24.90.20141023-1ubuntu1 [2263 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9 armhf 4.9.1-19ubuntu1 [4748 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid-proposed/main g++-4.9 armhf 4.9.1-19ubuntu1 [8703 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++-4.9-dev armhf 4.9.1-19ubuntu1 [1147 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc1 armhf 1:4.9.1-19ubuntu1 [40.0 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main libgmp10 armhf 2:6.0.0+dfsg-6 [195 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main libusb-0.1-4 armhf 2:0.1.12-25 [15.0 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main libacl1 armhf 2.2.52-2 [13.7 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgpg-error0 armhf 1.17-2 [28.0 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main libselinux1 armhf 2.3-2 [51.9 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsystemd-journal0 armhf 215-5ubuntu1 [49.0 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libp11-kit0 armhf 0.20.7-1 [66.2 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsqlite3-0 armhf 3.8.7-1 [316 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main libtasn1-6 armhf 4.2-2 [36.5 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main libdrm2 armhf 2.4.58-2 [20.9 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main plymouth armhf 0.9.0-0ubuntu8 [88.6 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid-proposed/main udev armhf 215-5ubuntu1 [832 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libudev1 armhf 215-5ubuntu1 [29.3 kB] Get:33 http://ftpmaster.internal/ubuntu/ vivid/main libplymouth4 armhf 0.9.0-0ubuntu8 [73.8 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main libgssapi-krb5-2 armhf 1.12.1+dfsg-11 [99.2 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5-3 armhf 1.12.1+dfsg-11 [228 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5support0 armhf 1.12.1+dfsg-11 [27.0 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid/main libk5crypto3 armhf 1.12.1+dfsg-11 [79.3 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-modules-db armhf 2.1.26.dfsg1-12 [13.0 kB] Get:39 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-2 armhf 2.1.26.dfsg1-12 [42.7 kB] Get:40 http://ftpmaster.internal/ubuntu/ vivid/main tzdata all 2014i-1 [182 kB] Get:41 http://ftpmaster.internal/ubuntu/ vivid/main ca-certificates all 20141019 [192 kB] Get:42 http://ftpmaster.internal/ubuntu/ vivid/main patch armhf 2.7.1-6 [78.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.4 MB in 4s (7285 kB/s) (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu8_armhf.deb ... Unpacking base-files (7.2ubuntu8) over (7.2ubuntu7) ... Setting up base-files (7.2ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../archives/grep_2.20-4_armhf.deb ... Unpacking grep (2.20-4) over (2.20-3) ... Setting up grep (2.20-4) ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../perl_5.20.1-2_armhf.deb ... Unpacking perl (5.20.1-2) over (5.20.1-1) ... Preparing to unpack .../perl-base_5.20.1-2_armhf.deb ... Unpacking perl-base (5.20.1-2) over (5.20.1-1) ... Setting up perl-base (5.20.1-2) ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../perl-modules_5.20.1-2_all.deb ... Unpacking perl-modules (5.20.1-2) over (5.20.1-1) ... Preparing to unpack .../libdb5.3_5.3.28-6_armhf.deb ... Unpacking libdb5.3:armhf (5.3.28-6) over (5.3.28-5) ... Setting up libdb5.3:armhf (5.3.28-6) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../libubsan0_4.9.1-19ubuntu1_armhf.deb ... Unpacking libubsan0:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../gcc-4.9-base_4.9.1-19ubuntu1_armhf.deb ... Unpacking gcc-4.9-base:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up gcc-4.9-base:armhf (4.9.1-19ubuntu1) ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.9.1-19ubuntu1_armhf.deb ... Unpacking libstdc++6:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up libstdc++6:armhf (4.9.1-19ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11279 files and directories currently installed.) Preparing to unpack .../libgomp1_4.9.1-19ubuntu1_armhf.deb ... Unpacking libgomp1:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libatomic1_4.9.1-19ubuntu1_armhf.deb ... Unpacking libatomic1:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libasan1_4.9.1-19ubuntu1_armhf.deb ... Unpacking libasan1:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libgcc-4.9-dev_4.9.1-19ubuntu1_armhf.deb ... Unpacking libgcc-4.9-dev:armhf (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../cpp-4.9_4.9.1-19ubuntu1_armhf.deb ... Unpacking cpp-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../binutils_2.24.90.20141023-1ubuntu1_armhf.deb ... Unpacking binutils (2.24.90.20141023-1ubuntu1) over (2.24.90.20141014-0ubuntu3) ... 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Setting up libusb-0.1-4:armhf (2:0.1.12-25) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11284 files and directories currently installed.) Preparing to unpack .../libacl1_2.2.52-2_armhf.deb ... Unpacking libacl1:armhf (2.2.52-2) over (2.2.52-1.1) ... Setting up libacl1:armhf (2.2.52-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11284 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.17-2_armhf.deb ... Unpacking libgpg-error0:armhf (1.17-2) over (1.13-4) ... Setting up libgpg-error0:armhf (1.17-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11284 files and directories currently installed.) Preparing to unpack .../libselinux1_2.3-2_armhf.deb ... Unpacking libselinux1:armhf (2.3-2) over (2.3-1build1) ... Setting up libselinux1:armhf (2.3-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11284 files and directories currently installed.) Preparing to unpack .../libsystemd-journal0_215-5ubuntu1_armhf.deb ... Unpacking libsystemd-journal0:armhf (215-5ubuntu1) over (208-8ubuntu8) ... Setting up libsystemd-journal0:armhf (215-5ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11284 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.20.7-1_armhf.deb ... Unpacking libp11-kit0:armhf (0.20.7-1) over (0.20.2-5) ... Preparing to unpack .../libsqlite3-0_3.8.7-1_armhf.deb ... Unpacking libsqlite3-0:armhf (3.8.7-1) over (3.8.6-1) ... Preparing to unpack .../libtasn1-6_4.2-2_armhf.deb ... Unpacking libtasn1-6:armhf (4.2-2) over (4.0-2) ... Preparing to unpack .../libdrm2_2.4.58-2_armhf.deb ... Unpacking libdrm2:armhf (2.4.58-2) over (2.4.56-1) ... Preparing to unpack .../plymouth_0.9.0-0ubuntu8_armhf.deb ... Unpacking plymouth (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../udev_215-5ubuntu1_armhf.deb ... Unpacking udev (215-5ubuntu1) over (208-8ubuntu8) ... Preparing to unpack .../libudev1_215-5ubuntu1_armhf.deb ... Unpacking libudev1:armhf (215-5ubuntu1) over (208-8ubuntu8) ... Preparing to unpack .../libplymouth4_0.9.0-0ubuntu8_armhf.deb ... Unpacking libplymouth4:armhf (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-11_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5-3_1.12.1+dfsg-11_armhf.deb ... Unpacking libkrb5-3:armhf (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5support0_1.12.1+dfsg-11_armhf.deb ... Unpacking libkrb5support0:armhf (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libk5crypto3_1.12.1+dfsg-11_armhf.deb ... Unpacking libk5crypto3:armhf (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-12_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-12_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../tzdata_2014i-1_all.deb ... Unpacking tzdata (2014i-1) over (2014h-2) ... Setting up tzdata (2014i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 25 18:40:22 UTC 2014. Universal Time is now: Sat Oct 25 18:40:22 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11289 files and directories currently installed.) Preparing to unpack .../ca-certificates_20141019_all.deb ... Unpacking ca-certificates (20141019) over (20140325) ... Preparing to unpack .../patch_2.7.1-6_armhf.deb ... Unpacking patch (2.7.1-6) over (2.7.1-5) ... Setting up libubsan0:armhf (4.9.1-19ubuntu1) ... Setting up libgomp1:armhf (4.9.1-19ubuntu1) ... Setting up libatomic1:armhf (4.9.1-19ubuntu1) ... Setting up libasan1:armhf (4.9.1-19ubuntu1) ... Setting up libgcc-4.9-dev:armhf (4.9.1-19ubuntu1) ... Setting up libgmp10:armhf (2:6.0.0+dfsg-6) ... Setting up cpp-4.9 (4.9.1-19ubuntu1) ... Setting up binutils (2.24.90.20141023-1ubuntu1) ... Setting up gcc-4.9 (4.9.1-19ubuntu1) ... Setting up libstdc++-4.9-dev:armhf (4.9.1-19ubuntu1) ... Setting up g++-4.9 (4.9.1-19ubuntu1) ... Setting up libp11-kit0:armhf (0.20.7-1) ... Setting up libsqlite3-0:armhf (3.8.7-1) ... Setting up libtasn1-6:armhf (4.2-2) ... Setting up libdrm2:armhf (2.4.58-2) ... Setting up libudev1:armhf (215-5ubuntu1) ... Setting up libplymouth4:armhf (0.9.0-0ubuntu8) ... Setting up udev (215-5ubuntu1) ... Installing new version of config file /etc/init.d/udev-finish ... A chroot environment has been detected, udev not started. update-initramfs: deferring update (trigger activated) Removing obsolete conffile /etc/udev/rules.d/README ... Setting up plymouth (0.9.0-0ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up libkrb5support0:armhf (1.12.1+dfsg-11) ... Setting up libk5crypto3:armhf (1.12.1+dfsg-11) ... Setting up libkrb5-3:armhf (1.12.1+dfsg-11) ... Setting up libgssapi-krb5-2:armhf (1.12.1+dfsg-11) ... Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-12) ... Setting up libsasl2-2:armhf (2.1.26.dfsg1-12) ... Setting up ca-certificates (20141019) ... Setting up patch (2.7.1-6) ... Setting up perl-modules (5.20.1-2) ... Setting up perl (5.20.1-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for initramfs-tools (0.103ubuntu8) ... Processing triggers for ca-certificates (20141019) ... Updating certificates in /etc/ssl/certs... 10 added, 5 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6505003', 'armhf', 'vivid-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=vivid-proposed', '--purpose=PRIMARY', '--architecture=armhf', '--comp=universe', 'mrbayes_3.2.3+dfsg-1.dsc'] Initiating build PACKAGEBUILD-6505003 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.2.0-68-highbank #102-Ubuntu SMP PREEMPT Tue Aug 12 22:53:28 UTC 2014 armv7l Automatic build of mrbayes_3.2.3+dfsg-1 on kishi06 by sbuild/armhf 1.170.5 Build started at 20141025-1840 ****************************************************************************** mrbayes_3.2.3+dfsg-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake Checking for already installed source dependencies... debhelper: missing libreadline-dev: missing mpi-default-dev: missing libhmsbeagle-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 intltool-debian libasprintf0c2 libcr0 libcroco3 libglib2.0-0 libhmsbeagle1 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpci-dev libpci3 libpipeline1 libreadline6-dev libsigsegv2 libtinfo-dev libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db openmpi-common po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff blcr-dkms libhwloc-contrib-plugins readline-doc pkg-config less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins 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 intltool-debian libasprintf0c2 libcr0 libcroco3 libglib2.0-0 libhmsbeagle-dev libhmsbeagle1 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpci-dev libpci3 libpipeline1 libreadline-dev libreadline6-dev libsigsegv2 libtinfo-dev libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db mpi-default-dev openmpi-common po-debconf zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 10.2 MB of archives. After this operation, 37.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main libmagic1 armhf 1:5.19-1ubuntu1.1 [198 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main libasprintf0c2 armhf 0.19.2-2ubuntu1 [6084 B] Get:3 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-0 armhf 2.42.0-2 [957 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid/main libpci3 armhf 1:3.2.1-1ubuntu9 [20.0 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid/main libpipeline1 armhf 1.3.1-1 [20.4 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libxml2 armhf 2.9.1+dfsg1-4ubuntu1 [496 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid/main groff-base armhf 1.22.2-8 [1039 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid/main bsdmainutils armhf 9.0.5ubuntu1 [195 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid/main man-db armhf 2.7.0.2-2 [839 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid/main libcroco3 armhf 0.6.8-3 [72.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid/main libltdl7 armhf 2.4.2-1.11 [32.5 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid/main libsigsegv2 armhf 2.10-4 [13.3 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid/main libunistring0 armhf 0.9.3-5ubuntu3 [251 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid/universe libhmsbeagle1 armhf 2.1.2-1 [48.8 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/universe libhwloc5 armhf 1.8-1ubuntu1 [64.5 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main file armhf 1:5.19-1ubuntu1.1 [19.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid/main gettext-base armhf 0.19.2-2ubuntu1 [44.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid/main m4 armhf 1.4.17-4 [178 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid/main autoconf all 2.69-8 [321 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main autotools-dev all 20140911.1 [39.6 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main automake all 1:1.14.1-3ubuntu1 [510 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main gettext armhf 0.19.2-2ubuntu1 [792 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main po-debconf all 1.0.16+nmu3 [207 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main dh-apparmor all 2.8.98-0ubuntu2 [11.0 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main debhelper all 9.20141003ubuntu1 [726 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/universe libcr0 armhf 0.8.5-2.1 [15.9 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main zlib1g-dev armhf 1:1.2.8.dfsg-1ubuntu1 [176 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main libpci-dev armhf 1:3.2.1-1ubuntu9 [40.2 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main libtinfo-dev armhf 5.9+20140712-2ubuntu1 [66.8 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main libreadline6-dev armhf 6.3-8ubuntu1 [109 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid/main libreadline-dev armhf 6.3-8ubuntu1 [1042 B] Get:33 http://ftpmaster.internal/ubuntu/ vivid/universe libtorque2 armhf 2.4.16+dfsg-1.4ubuntu1 [65.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main libxml2-dev armhf 2.9.1+dfsg1-4ubuntu1 [572 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/universe openmpi-common all 1.6.5-8 [101 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid/universe libhmsbeagle-dev armhf 2.1.2-1 [136 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid/universe libhwloc-dev armhf 1.8-1ubuntu1 [116 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/main libibverbs1 armhf 1.1.8-1ubuntu1 [21.8 kB] Get:39 http://ftpmaster.internal/ubuntu/ vivid/main libibverbs-dev armhf 1.1.8-1ubuntu1 [74.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ vivid/universe libopenmpi1.6 armhf 1.6.5-8 [1236 kB] Get:41 http://ftpmaster.internal/ubuntu/ vivid/universe libopenmpi-dev armhf 1.6.5-8 [378 kB] Get:42 http://ftpmaster.internal/ubuntu/ vivid/universe mpi-default-dev armhf 1.0.2+nmu2 [4008 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.2 MB in 1s (5304 kB/s) Selecting previously unselected package libmagic1:armhf. (Reading database ... 11294 files and directories currently installed.) Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1.1_armhf.deb ... Unpacking libmagic1:armhf (1:5.19-1ubuntu1.1) ... Selecting previously unselected package libasprintf0c2:armhf. Preparing to unpack .../libasprintf0c2_0.19.2-2ubuntu1_armhf.deb ... Unpacking libasprintf0c2:armhf (0.19.2-2ubuntu1) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../libglib2.0-0_2.42.0-2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.42.0-2) ... Selecting previously unselected package libpci3:armhf. Preparing to unpack .../libpci3_1%3a3.2.1-1ubuntu9_armhf.deb ... Unpacking libpci3:armhf (1:3.2.1-1ubuntu9) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../libpipeline1_1.3.1-1_armhf.deb ... Unpacking libpipeline1:armhf (1.3.1-1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../libxml2_2.9.1+dfsg1-4ubuntu1_armhf.deb ... 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Setting up libmagic1:armhf (1:5.19-1ubuntu1.1) ... Setting up libasprintf0c2:armhf (0.19.2-2ubuntu1) ... Setting up libglib2.0-0:armhf (2.42.0-2) ... No schema files found: doing nothing. Setting up libpci3:armhf (1:3.2.1-1ubuntu9) ... Setting up libpipeline1:armhf (1.3.1-1) ... Setting up libxml2:armhf (2.9.1+dfsg1-4ubuntu1) ... Setting up groff-base (1.22.2-8) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.7.0.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:armhf (0.6.8-3) ... Setting up libltdl7:armhf (2.4.2-1.11) ... Setting up libsigsegv2:armhf (2.10-4) ... Setting up libunistring0:armhf (0.9.3-5ubuntu3) ... Setting up libhmsbeagle1 (2.1.2-1) ... Setting up libhwloc5:armhf (1.8-1ubuntu1) ... Setting up file (1:5.19-1ubuntu1.1) ... Setting up gettext-base (0.19.2-2ubuntu1) ... Setting up m4 (1.4.17-4) ... Setting up autoconf (2.69-8) ... Setting up autotools-dev (20140911.1) ... Setting up automake (1:1.14.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.2-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.98-0ubuntu2) ... Setting up debhelper (9.20141003ubuntu1) ... Setting up libcr0 (0.8.5-2.1) ... Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1ubuntu1) ... Setting up libpci-dev (1:3.2.1-1ubuntu9) ... Setting up libtinfo-dev:armhf (5.9+20140712-2ubuntu1) ... Setting up libreadline6-dev:armhf (6.3-8ubuntu1) ... Setting up libreadline-dev:armhf (6.3-8ubuntu1) ... Setting up libtorque2 (2.4.16+dfsg-1.4ubuntu1) ... Setting up libxml2-dev:armhf (2.9.1+dfsg1-4ubuntu1) ... Setting up openmpi-common (1.6.5-8) ... Setting up libhmsbeagle-dev (2.1.2-1) ... Setting up libhwloc-dev:armhf (1.8-1ubuntu1) ... Setting up libibverbs1 (1.1.8-1ubuntu1) ... Setting up libibverbs-dev (1.1.8-1ubuntu1) ... Setting up libopenmpi1.6 (1.6.5-8) ... Setting up libopenmpi-dev (1.6.5-8) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up mpi-default-dev (1.0.2+nmu2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-10ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-19ubuntu1 g++-4.9_4.9.1-19ubuntu1 binutils_2.24.90.20141023-1ubuntu1 libstdc++-4.9-dev_4.9.1-19ubuntu1 libstdc++6_4.9.1-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Sat Oct 25 08:16:32 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.3+dfsg-1.dsc dpkg-source: info: extracting mrbayes in mrbayes-3.2.3+dfsg dpkg-source: info: unpacking mrbayes_3.2.3+dfsg.orig.tar.xz dpkg-source: info: unpacking mrbayes_3.2.3+dfsg-1.debian.tar.xz dpkg-source: info: applying as-needed.patch dpkg-source: info: applying ldlibs.patch dpkg-buildpackage: source package mrbayes dpkg-buildpackage: source version 3.2.3+dfsg-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build mrbayes-3.2.3+dfsg dpkg-buildpackage: host architecture armhf /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-3.2.3+dfsg' ( cd src ; /usr/bin/make -f Makefile.in distclean ) make[2]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg/src' rm -f *.o *~ mb rm -rf Makefile config.log config.status config.h *.cache make[2]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg/src' rm -f src/configure rm -f mb mb-mpi src/mb make[1]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_clean -O--sourcedirectory=src debian/rules build-arch dh build-arch --sourcedirectory=src dh_testdir -a -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg' #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/libhmsbeagle/beagle.h... no checking for /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... 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-3.2.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make[2]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg/src' mpicc -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c mpicc -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o mcmc.o model.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm make[2]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg/src' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg/src' rm -f *.o *~ mb make[2]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg/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/libhmsbeagle/beagle.h... no checking for /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... 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-3.2.3+dfsg/src' gcc -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c gcc -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o mcmc.o model.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm make[2]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg/src' mv src/mb . make[1]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_auto_test -a -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 debian/rules override_dh_auto_install make[1]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg' echo "Do not try to install to /usr/local/bin" Do not try to install to /usr/local/bin make[1]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_install -a -O--sourcedirectory=src dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src dh_installman -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_link -a -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_fixperms -a -O--sourcedirectory=src debian/rules override_dh_strip make[1]: Entering directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_strip --dbg-package=mrbayes-dbg dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: mrbayes mrbayes-mpi mrbayes-dbg dh_strip debug symbol extraction: not adding gnu debuglinks since --dbg-package is given dh_strip debug symbol extraction: packages to act on: mrbayes mrbayes-mpi mrbayes-dbg dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 we have -dbg package(s), not installing anything into ddeb find: `/build/buildd/mrbayes-3.2.3+dfsg/debian/mrbayes-dbgsym': No such file or directory dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `mrbayes-dbgsym' in `../mrbayes-dbgsym_3.2.3+dfsg-1_armhf.ddeb'. Using buildid for compat level >= 9 we have -dbg package(s), not installing anything into ddeb find: `/build/buildd/mrbayes-3.2.3+dfsg/debian/mrbayes-mpi-dbgsym': No such file or directory dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `mrbayes-mpi-dbgsym' in `../mrbayes-mpi-dbgsym_3.2.3+dfsg-1_armhf.ddeb'. make[1]: Leaving directory '/build/buildd/mrbayes-3.2.3+dfsg' dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src INFO: pkgstriptranslations version 121 pkgstriptranslations: processing mrbayes (in debian/mrbayes); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mrbayes/DEBIAN/control, package mrbayes, directory debian/mrbayes pkgstripfiles: Truncating usr/share/doc/mrbayes/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package mrbayes took 0 s dpkg-deb: warning: 'debian/mrbayes/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `mrbayes' in `../mrbayes_3.2.3+dfsg-1_armhf.deb'. INFO: pkgstriptranslations version 121 pkgstriptranslations: processing mrbayes-mpi (in debian/mrbayes-mpi); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mrbayes-mpi/DEBIAN/control, package mrbayes-mpi, directory debian/mrbayes-mpi pkgstripfiles: Truncating usr/share/doc/mrbayes-mpi/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package mrbayes-mpi took 0 s dpkg-deb: warning: 'debian/mrbayes-mpi/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `mrbayes-mpi' in `../mrbayes-mpi_3.2.3+dfsg-1_armhf.deb'. INFO: pkgstriptranslations version 121 pkgstriptranslations: processing mrbayes-dbg (in debian/mrbayes-dbg); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mrbayes-dbg/DEBIAN/control, package mrbayes-dbg, directory debian/mrbayes-dbg Searching for duplicated docs in dependency mrbayes... symlinking changelog.Debian.gz in mrbayes-dbg to file in mrbayes pkgstripfiles: PNG optimization for package mrbayes-dbg took 0 s dpkg-deb: warning: 'debian/mrbayes-dbg/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `mrbayes-dbg' in `../mrbayes-dbg_3.2.3+dfsg-1_armhf.deb'. dpkg-genchanges -B -mUbuntu/armhf Build Daemon >../mrbayes_3.2.3+dfsg-1_armhf.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build mrbayes-3.2.3+dfsg dpkg-buildpackage: binary-only upload (no source included) ****************************************************************************** Build finished at 20141025-1852 Publishing debug debs. chroot-autobuild/build/buildd/mrbayes_3.2.3+dfsg-1_armhf.deb: new debian package, version 2.0. size 495238 bytes: control archive= 945 bytes. 921 bytes, 19 lines control 318 bytes, 5 lines md5sums Package: mrbayes Version: 3.2.3+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1246 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_3.2.3+dfsg-1_armhf.deb: new debian package, version 2.0. size 505272 bytes: control archive= 1063 bytes. 1077 bytes, 22 lines control 399 bytes, 6 lines md5sums Package: mrbayes-mpi Source: mrbayes Version: 3.2.3+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1271 Depends: libc6 (>= 2.7), libhmsbeagle1, libopenmpi1.6, 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_3.2.3+dfsg-1_armhf.deb: new debian package, version 2.0. size 1667226 bytes: control archive= 1057 bytes. 1269 bytes, 24 lines control 282 bytes, 3 lines md5sums Package: mrbayes-dbg Source: mrbayes Version: 3.2.3+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1796 Depends: mrbayes (= 3.2.3+dfsg-1) | mrbayes-mpi (= 3.2.3+dfsg-1) Breaks: mrbayes (>> 3.2.3+dfsg-1), mrbayes (<< 3.2.3+dfsg-1), mrbayes-mpi (>> 3.2.3+dfsg-1), mrbayes-mpi (<< 3.2.3+dfsg-1) 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_3.2.3+dfsg-1_armhf.deb: drwxr-xr-x root/root 0 2014-10-25 18:52 ./ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/man/man1/ -rw-r--r-- root/root 206 2014-10-25 18:52 ./usr/share/man/man1/mb.1.gz drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/mrbayes/ -rw-r--r-- root/root 1628 2014-10-25 18:52 ./usr/share/doc/mrbayes/changelog.Debian.gz -rw-r--r-- root/root 311 2013-09-12 08:57 ./usr/share/doc/mrbayes/README.Debian -rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes/copyright drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/bin/ -rwxr-xr-x root/root 1235180 2014-10-25 18:52 ./usr/bin/mb chroot-autobuild/build/buildd/mrbayes-mpi_3.2.3+dfsg-1_armhf.deb: drwxr-xr-x root/root 0 2014-10-25 18:52 ./ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/man/man1/ -rw-r--r-- root/root 226 2014-10-25 18:52 ./usr/share/man/man1/mb-mpi.1.gz drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/mrbayes-mpi/ -rw-r--r-- root/root 1630 2014-10-25 18:52 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz -rw-r--r-- root/root 348 2013-09-12 08:57 ./usr/share/doc/mrbayes-mpi/README.Debian -rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes-mpi/copyright drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/mrbayes-mpi/ -rwxr-xr-x root/root 1251612 2014-10-25 18:52 ./usr/lib/mrbayes-mpi/mb-mpi drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/bin/ -rwxr-xr-x root/root 162 2013-09-12 08:57 ./usr/bin/mb-mpi chroot-autobuild/build/buildd/mrbayes-dbg_3.2.3+dfsg-1_armhf.deb: drwxr-xr-x root/root 0 2014-10-25 18:52 ./ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/share/doc/mrbayes-dbg/ -rw-r--r-- root/root 1482 2013-09-12 08:57 ./usr/share/doc/mrbayes-dbg/copyright drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/debug/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/debug/.build-id/78/ -rw-r--r-- root/root 888620 2014-10-25 18:52 ./usr/lib/debug/.build-id/78/23b78a8df91883bd64f6e3f3f746da01cfede5.debug drwxr-xr-x root/root 0 2014-10-25 18:52 ./usr/lib/debug/.build-id/69/ -rw-r--r-- root/root 902056 2014-10-25 18:52 ./usr/lib/debug/.build-id/69/081c55653f8b66836acd9bfa3c7677ac12b88e.debug lrwxrwxrwx root/root 0 2014-10-25 18:52 ./usr/share/doc/mrbayes-dbg/changelog.Debian.gz -> ../mrbayes/changelog.Debian.gz mrbayes_3.2.3+dfsg-1_armhf.changes: Format: 1.8 Date: Sat, 25 Oct 2014 09:38:38 +0200 Source: mrbayes Binary: mrbayes mrbayes-mpi mrbayes-dbg mrbayes-doc Architecture: armhf Version: 3.2.3+dfsg-1 Distribution: vivid-proposed Urgency: medium Maintainer: Ubuntu/armhf Build Daemon Changed-By: Andreas Tille 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 (3.2.3+dfsg-1) unstable; urgency=medium . * New upstream version * d/rules - use xz in get-orig-source target - drop redundant xz compression for binary package * Adapt get-orig-source script * cme fix dpkg-control Checksums-Sha1: 3fc461dae274864b999c5c914bcb0fb85c951460 495238 mrbayes_3.2.3+dfsg-1_armhf.deb 195be0b277eb3fdee535582efc3a167593ed5c03 505272 mrbayes-mpi_3.2.3+dfsg-1_armhf.deb f131b6623359807a2201b5c3631ffeb5c55e5cdb 1667226 mrbayes-dbg_3.2.3+dfsg-1_armhf.deb Checksums-Sha256: 09ee13ad7823865cdecedc011c4ebb1e00776842da7261e7c02e444281bcd12f 495238 mrbayes_3.2.3+dfsg-1_armhf.deb fe37c3060e4843cea6e71c960276d631e5a0e0613aa4606eb1f2bd66b83098a7 505272 mrbayes-mpi_3.2.3+dfsg-1_armhf.deb a9caa3d9d3a6ee5b62f62828073310dae6f4bee3f9c5c60acb9893a3497bc3ea 1667226 mrbayes-dbg_3.2.3+dfsg-1_armhf.deb Files: f3dc91c49da5b8b83e7ffd8cbfa15ea6 495238 science optional mrbayes_3.2.3+dfsg-1_armhf.deb 76be37411560d2675388e22eaa882d1c 505272 science optional mrbayes-mpi_3.2.3+dfsg-1_armhf.deb 500bb4ef94e70203fdaf97276e8512f7 1667226 debug extra mrbayes-dbg_3.2.3+dfsg-1_armhf.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20141025-1852 Build needed 00:11:18, 27416k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6505003'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6505003/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6505003'] Unmounting chroot for build PACKAGEBUILD-6505003... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6505003'] Removing build PACKAGEBUILD-6505003