RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-04 3.19.0-28-generic #30~14.04.1-Ubuntu SMP Tue Sep 1 09:32:55 UTC 2015 x86_64 Buildd toolchain package versions: launchpad-buildd_133 python-lpbuildd_133 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.4 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 15 Sep 16:50:03 ntpdate[1649]: adjust time server 10.211.37.1 offset 0.090627 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-7904694', '/home/buildd/filecache-default/bcd5dc063ce51e1147d70d5a7a54c6f9cc3d3ea4'] Unpacking chroot for build PACKAGEBUILD-7904694 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-7904694'] Mounting chroot for build PACKAGEBUILD-7904694 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-7904694', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty main', 'deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main', 'deb http://ftpmaster.internal/ubuntu trusty main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-7904694 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-7904694', 'amd64'] Updating debian chroot for build PACKAGEBUILD-7904694 Ign http://ftpmaster.internal trusty InRelease Ign http://ppa.launchpad.net trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://ppa.launchpad.net trusty InRelease Ign http://ftpmaster.internal trusty-updates InRelease Get:1 http://ppa.launchpad.net trusty Release.gpg [316 B] Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ppa.launchpad.net trusty Release.gpg [316 B] Get:4 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:6 http://ppa.launchpad.net trusty Release [15.1 kB] Get:7 http://ftpmaster.internal trusty Release [58.5 kB] Ign http://ppa.launchpad.net trusty Release Get:8 http://ppa.launchpad.net trusty Release [15.1 kB] Get:9 http://ftpmaster.internal trusty-security Release [63.5 kB] Get:10 http://ftpmaster.internal trusty-updates Release [63.5 kB] Get:11 http://ftpmaster.internal trusty/main amd64 Packages [1350 kB] Get:12 http://ftpmaster.internal trusty/restricted amd64 Packages [13.0 kB] Get:13 http://ftpmaster.internal trusty/universe amd64 Packages [5859 kB] Ign http://ppa.launchpad.net trusty Release Get:14 http://ppa.launchpad.net trusty/main amd64 Packages [51.4 kB] Get:15 http://ppa.launchpad.net trusty/main Translation-en [47.5 kB] Get:16 http://ppa.launchpad.net trusty/main amd64 Packages [8013 B] Get:17 http://ppa.launchpad.net trusty/main Translation-en [7147 B] Get:18 http://ftpmaster.internal trusty/multiverse amd64 Packages [132 kB] Get:19 http://ftpmaster.internal trusty/main Translation-en [762 kB] Get:20 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:21 http://ftpmaster.internal trusty/restricted Translation-en [3457 B] Get:22 http://ftpmaster.internal trusty/universe Translation-en [4089 kB] Get:23 http://ftpmaster.internal trusty-security/main amd64 Packages [343 kB] Get:24 http://ftpmaster.internal trusty-security/restricted amd64 Packages [8875 B] Get:25 http://ftpmaster.internal trusty-security/universe amd64 Packages [116 kB] Get:26 http://ftpmaster.internal trusty-security/multiverse amd64 Packages [3686 B] Get:27 http://ftpmaster.internal trusty-security/main Translation-en [187 kB] Get:28 http://ftpmaster.internal trusty-security/multiverse Translation-en [1679 B] Get:29 http://ftpmaster.internal trusty-security/restricted Translation-en [2266 B] Get:30 http://ftpmaster.internal trusty-security/universe Translation-en [67.8 kB] Get:31 http://ftpmaster.internal trusty-updates/main amd64 Packages [619 kB] Get:32 http://ftpmaster.internal trusty-updates/restricted amd64 Packages [15.4 kB] Get:33 http://ftpmaster.internal trusty-updates/universe amd64 Packages [312 kB] Get:34 http://ftpmaster.internal trusty-updates/multiverse amd64 Packages [11.9 kB] Get:35 http://ftpmaster.internal trusty-updates/main Translation-en [300 kB] Get:36 http://ftpmaster.internal trusty-updates/multiverse Translation-en [6148 B] Get:37 http://ftpmaster.internal trusty-updates/restricted Translation-en [3560 B] Get:38 http://ftpmaster.internal trusty-updates/universe Translation-en [166 kB] Fetched 14.8 MB in 7s (2093 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net trusty Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: GPG error: http://ppa.launchpad.net trusty Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5E25F516B04C661B Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files bash binutils bsdutils ca-certificates coreutils cpio cpp-4.8 dpkg dpkg-dev e2fslibs e2fsprogs g++-4.8 gcc-4.8 gcc-4.8-base gcc-4.9-base gnupg gpgv ifupdown initramfs-tools initramfs-tools-bin initscripts iproute2 libapt-pkg4.12 libasan0 libasn1-8-heimdal libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcgmanager0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm2 libgcc-4.8-dev libgcc1 libgcrypt11 libgnutls26 libgomp1 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libjson-c2 libjson0 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libpcre3 libplymouth2 libprocps3 libquadmath0 libroken18-heimdal libselinux1 libsepol1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-4.8-dev libstdc++6 libtasn1-6 libtsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd patch pkg-create-dbgsym plymouth procps sysv-rc sysvinit-utils tzdata udev upstart util-linux 93 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 55.7 MB of archives. After this operation, 7493 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ trusty-updates/main base-files amd64 7.2ubuntu5.3 [60.9 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty-security/main bash amd64 4.3-7ubuntu1.5 [576 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-security/main coreutils amd64 8.21-1ubuntu5.1 [1089 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg amd64 1.17.5ubuntu5.4 [1954 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty-security/main libpcre3 amd64 1:8.31-2ubuntu2.1 [144 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-updates/main libselinux1 amd64 2.2.2-1ubuntu0.1 [58.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty-updates/main sysv-rc all 2.88dsf-41ubuntu6.2 [36.4 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty-updates/main sysvinit-utils amd64 2.88dsf-41ubuntu6.2 [53.1 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty-updates/main mount amd64 2.20.1-5.1ubuntu20.6 [114 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty-updates/main passwd amd64 1:4.1.5.1-1ubuntu9.1 [755 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty-updates/main initscripts amd64 2.88dsf-41ubuntu6.2 [27.7 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-security/main libdbus-1-3 amd64 1.6.18-0ubuntu4.3 [132 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson-c2 amd64 0.11-3ubuntu1.2 [22.0 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty-updates/main libuuid1 amd64 2.20.1-5.1ubuntu20.6 [10.9 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty-updates/main libblkid1 amd64 2.20.1-5.1ubuntu20.6 [62.5 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcgmanager0 amd64 0.24-0ubuntu7.3 [29.2 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty-security/main tzdata all 2015f-0ubuntu0.14.04 [171 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty-updates/main util-linux amd64 2.20.1-5.1ubuntu20.6 [458 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty-updates/main libprocps3 amd64 1:3.3.9-1ubuntu2.2 [31.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-updates/main procps amd64 1:3.3.9-1ubuntu2.2 [209 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-updates/main udev amd64 204-5ubuntu20.13 [735 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty-updates/main libudev1 amd64 204-5ubuntu20.13 [33.2 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty-updates/main iproute2 amd64 3.12.0-2ubuntu1 [401 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-updates/main ifupdown amd64 0.7.47.2ubuntu4.1 [52.1 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty-security/main libjson0 amd64 0.11-3ubuntu1.2 [1080 B] Get:26 http://ftpmaster.internal/ubuntu/ trusty-updates/main upstart amd64 1.12.1-0ubuntu4.2 [390 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6-dev amd64 2.19-0ubuntu6.6 [1910 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-dev-bin amd64 2.19-0ubuntu6.6 [68.9 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty-security/main linux-libc-dev amd64 3.13.0-63.103 [777 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty-security/main libc-bin amd64 2.19-0ubuntu6.6 [1168 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.9-base amd64 4.9.1-0ubuntu1 [14.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgcc1 amd64 1:4.9.1-0ubuntu1 [39.2 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty-security/main libc6 amd64 2.19-0ubuntu6.6 [4735 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty-security/main e2fslibs amd64 1.42.9-3ubuntu1.2 [183 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty-security/main e2fsprogs amd64 1.42.9-3ubuntu1.2 [668 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty-updates/main login amd64 1:4.1.5.1-1ubuntu9.1 [301 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty-updates/main libtsan0 amd64 4.8.4-2ubuntu1~14.04 [94.7 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgomp1 amd64 4.8.4-2ubuntu1~14.04 [23.1 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty-updates/main libitm1 amd64 4.8.4-2ubuntu1~14.04 [28.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty-updates/main libatomic1 amd64 4.8.4-2ubuntu1~14.04 [8650 B] Get:41 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasan0 amd64 4.8.4-2ubuntu1~14.04 [63.0 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty-updates/main libquadmath0 amd64 4.8.4-2ubuntu1~14.04 [126 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty-updates/main g++-4.8 amd64 4.8.4-2ubuntu1~14.04 [15.0 MB] Get:44 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.8 amd64 4.8.4-2ubuntu1~14.04 [5049 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty-updates/main cpp-4.8 amd64 4.8.4-2ubuntu1~14.04 [4597 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty-updates/main binutils amd64 2.24-5ubuntu13 [2076 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty-updates/main libstdc++-4.8-dev amd64 4.8.4-2ubuntu1~14.04 [1052 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgcc-4.8-dev amd64 4.8.4-2ubuntu1~14.04 [1687 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty-updates/main gcc-4.8-base amd64 4.8.4-2ubuntu1~14.04 [15.9 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty-updates/main libstdc++6 amd64 4.8.4-2ubuntu1~14.04 [259 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty-updates/main libapt-pkg4.12 amd64 1.0.1ubuntu2.10 [637 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty-security/main gpgv amd64 1.4.16-1ubuntu2.3 [161 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty-security/main gnupg amd64 1.4.16-1ubuntu2.3 [611 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty-updates/main apt amd64 1.0.1ubuntu2.10 [952 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-updates/main bsdutils amd64 1:2.20.1-5.1ubuntu20.6 [33.8 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty-security/main libcomerr2 amd64 1.42.9-3ubuntu1.2 [62.8 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty-updates/main libmount1 amd64 2.20.1-5.1ubuntu20.6 [60.2 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty-updates/main libsepol1 amd64 2.2-1ubuntu0.1 [107 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty-security/main libss2 amd64 1.42.9-3ubuntu1.2 [67.1 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty-security/main libgcrypt11 amd64 1.5.3-2ubuntu4.2 [239 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty-security/main libtasn1-6 amd64 3.4-3ubuntu0.3 [43.6 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty-security/main libgnutls26 amd64 2.12.23-12ubuntu2.2 [393 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty-security/main libsqlite3-0 amd64 3.8.2-1ubuntu2.1 [342 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty-security/main libssl1.0.0 amd64 1.0.1f-1ubuntu2.15 [826 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty-updates/main libdrm2 amd64 2.4.60-2~ubuntu14.04.1 [23.5 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools all 0.103ubuntu4.2 [44.3 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty-updates/main initramfs-tools-bin amd64 0.103ubuntu4.2 [8922 B] Get:68 http://ftpmaster.internal/ubuntu/ trusty-security/main cpio amd64 2.11+dfsg-1ubuntu1.1 [73.3 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty-updates/main plymouth amd64 0.8.8-0ubuntu17.1 [98.6 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty-updates/main libplymouth2 amd64 0.8.8-0ubuntu17.1 [76.8 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty-updates/main libroken18-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [40.0 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasn1-8-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [161 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty-security/main libk5crypto3 amd64 1.12+dfsg-2ubuntu5.1 [79.8 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty-security/main libgssapi-krb5-2 amd64 1.12+dfsg-2ubuntu5.1 [113 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5-3 amd64 1.12+dfsg-2ubuntu5.1 [262 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty-security/main libkrb5support0 amd64 1.12+dfsg-2ubuntu5.1 [30.4 kB] Get:77 http://ftpmaster.internal/ubuntu/ trusty-updates/main libhcrypto4-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [83.9 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty-updates/main libheimbase1-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [28.9 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty-updates/main libwind0-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [47.8 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty-updates/main libhx509-5-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [104 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty-updates/main libkrb5-26-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [196 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty-updates/main libheimntlm0-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [15.2 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgssapi3-heimdal amd64 1.6~git20131207+dfsg-1ubuntu1.1 [89.8 kB] Get:84 http://ftpmaster.internal/ubuntu/ trusty-security/main libldap-2.4-2 amd64 2.4.31-1+nmu2ubuntu8.1 [153 kB] Get:85 http://ftpmaster.internal/ubuntu/ trusty-security/main libcurl3-gnutls amd64 7.35.0-1ubuntu2.5 [165 kB] Get:86 http://ftpmaster.internal/ubuntu/ trusty-security/main multiarch-support amd64 2.19-0ubuntu6.6 [4486 B] Get:87 http://ftpmaster.internal/ubuntu/ trusty-updates/main apt-transport-https amd64 1.0.1ubuntu2.10 [25.1 kB] Get:88 http://ftpmaster.internal/ubuntu/ trusty-security/main openssl amd64 1.0.1f-1ubuntu2.15 [489 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty-security/main ca-certificates all 20141019ubuntu0.14.04.1 [189 kB] Get:90 http://ftpmaster.internal/ubuntu/ trusty-security/main dpkg-dev all 1.17.5ubuntu5.4 [726 kB] Get:91 http://ftpmaster.internal/ubuntu/ trusty-security/main libdpkg-perl all 1.17.5ubuntu5.4 [179 kB] Get:92 http://ftpmaster.internal/ubuntu/ trusty-security/main patch amd64 2.7.1-4ubuntu2.3 [86.4 kB] Get:93 http://ftpmaster.internal/ubuntu/ trusty-security/main pkg-create-dbgsym all 0.67~trusty [8844 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.7 MB in 9s (5766 kB/s) (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu5.3_amd64.deb ... Unpacking base-files (7.2ubuntu5.3) over (7.2ubuntu5) ... Setting up base-files (7.2ubuntu5.3) ... 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 ... 11788 files and directories currently installed.) Preparing to unpack .../bash_4.3-7ubuntu1.5_amd64.deb ... Unpacking bash (4.3-7ubuntu1.5) over (4.3-6ubuntu1) ... Setting up bash (4.3-7ubuntu1.5) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 11788 files and directories currently installed.) Preparing to unpack .../coreutils_8.21-1ubuntu5.1_amd64.deb ... Unpacking coreutils (8.21-1ubuntu5.1) over (8.21-1ubuntu5) ... Setting up coreutils (8.21-1ubuntu5.1) ... 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Installing new version of config file /etc/cron.daily/upstart ... Setting up libc-dev-bin (2.19-0ubuntu6.6) ... Setting up linux-libc-dev:amd64 (3.13.0-63.103) ... Setting up libc6-dev:amd64 (2.19-0ubuntu6.6) ... Setting up libtsan0:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libgomp1:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libitm1:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libatomic1:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libasan0:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libquadmath0:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up cpp-4.8 (4.8.4-2ubuntu1~14.04) ... Setting up binutils (2.24-5ubuntu13) ... Setting up libgcc-4.8-dev:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up gcc-4.8 (4.8.4-2ubuntu1~14.04) ... Setting up libstdc++-4.8-dev:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up g++-4.8 (4.8.4-2ubuntu1~14.04) ... Setting up libgcrypt11:amd64 (1.5.3-2ubuntu4.2) ... Setting up libtasn1-6:amd64 (3.4-3ubuntu0.3) ... Setting up libgnutls26:amd64 (2.12.23-12ubuntu2.2) ... Setting up libsqlite3-0:amd64 (3.8.2-1ubuntu2.1) ... Setting up libssl1.0.0:amd64 (1.0.1f-1ubuntu2.15) ... Setting up libdrm2:amd64 (2.4.60-2~ubuntu14.04.1) ... Setting up initramfs-tools-bin (0.103ubuntu4.2) ... Setting up cpio (2.11+dfsg-1ubuntu1.1) ... Setting up initramfs-tools (0.103ubuntu4.2) ... update-initramfs: deferring update (trigger activated) Setting up libplymouth2:amd64 (0.8.8-0ubuntu17.1) ... Setting up plymouth (0.8.8-0ubuntu17.1) ... update-initramfs: deferring update (trigger activated) Setting up libroken18-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libasn1-8-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libkrb5support0:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libk5crypto3:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libkrb5-3:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libgssapi-krb5-2:amd64 (1.12+dfsg-2ubuntu5.1) ... Setting up libhcrypto4-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libheimbase1-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libwind0-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libhx509-5-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libkrb5-26-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libheimntlm0-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libgssapi3-heimdal:amd64 (1.6~git20131207+dfsg-1ubuntu1.1) ... Setting up libldap-2.4-2:amd64 (2.4.31-1+nmu2ubuntu8.1) ... Setting up libcurl3-gnutls:amd64 (7.35.0-1ubuntu2.5) ... Setting up apt-transport-https (1.0.1ubuntu2.10) ... Setting up openssl (1.0.1f-1ubuntu2.15) ... Setting up ca-certificates (20141019ubuntu0.14.04.1) ... Setting up libdpkg-perl (1.17.5ubuntu5.4) ... Setting up patch (2.7.1-4ubuntu2.3) ... Setting up dpkg-dev (1.17.5ubuntu5.4) ... Setting up pkg-create-dbgsym (0.67~trusty) ... Processing triggers for libc-bin (2.19-0ubuntu6.6) ... Processing triggers for initramfs-tools (0.103ubuntu4.2) ... Processing triggers for ca-certificates (20141019ubuntu0.14.04.1) ... Updating certificates in /etc/ssl/certs... 17 added, 8 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-7904694', 'amd64', 'trusty', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=trusty', '--purge=never', '--nolog', 'genomicalignments_1.4.1-1cran1ppa0.dsc'] Initiating build PACKAGEBUILD-7904694 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.19.0-28-generic #30~14.04.1-Ubuntu SMP Tue Sep 1 09:32:55 UTC 2015 x86_64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-04.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ genomicalignments 1.4.1-1cran1ppa0 (amd64) 15 Sep 2015 16:50 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: genomicalignments Version: 1.4.1-1cran1ppa0 Source Version: 1.4.1-1cran1ppa0 Distribution: trusty Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/genomicalignments-8pMa_0/genomicalignments-1.4.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/genomicalignments-8pMa_0' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-7904694/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── genomicalignments_1.4.1-1cran1ppa0.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-nhOQdu/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11837 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), r-base-dev, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-biocparallel, xvfb, xauth, xfonts-base, r-base-core, debhelper (>> 4.1.0), cdbs Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), r-base-dev, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-biocparallel, xvfb, xauth, xfonts-base, r-base-core, debhelper (>> 4.1.0), cdbs dpkg-deb: building package `sbuild-build-depends-genomicalignments-dummy' in `/«BUILDDIR»/resolver-KAQ9Xq/apt_archive/sbuild-build-depends-genomicalignments-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en Reading package lists... Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install genomicalignments build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-apparmor dh-translations file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base intltool intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfontenc1 libfreetype6 libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmagic1 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsigsegv2 libsm6 libtcl8.6 libthai-data libthai0 libtiff5 libtinfo-dev libtk8.6 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxfont1 libxft2 libxkbfile1 libxml-parser-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrender1 libxshmfence1 libxss1 libxt6 libxxf86vm1 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-snow ucf unzip x11-common x11-xkb-utils xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xserver-common xvfb zip zlib1g-dev Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts dh-make apparmor-easyprof gettext-doc gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc libgfortran3-dbg groff libdata-dump-perl libcrypt-ssleay-perl liblzma-doc ncurses-doc ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp tcl8.6 tk8.6 libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc binfmt-support r-doc-info r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo r-cran-rmpi r-cran-rsprng r-cran-rlecuyer gvfs-bin xfs xserver Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libgl1-mesa-dri libglib2.0-data shared-mime-info libhtml-format-perl libio-socket-inet6-perl libio-socket-ip-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core libmail-sendmail-perl r-recommended r-doc-html libfile-mimeinfo-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-apparmor dh-translations file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base intltool intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfontenc1 libfreetype6 libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev libmagic1 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsigsegv2 libsm6 libtcl8.6 libthai-data libthai0 libtiff5 libtinfo-dev libtk8.6 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxfont1 libxft2 libxkbfile1 libxml-parser-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrender1 libxshmfence1 libxss1 libxt6 libxxf86vm1 m4 man-db mime-support netbase po-debconf python python-minimal python-scour python2.7 python2.7-minimal r-base-core r-base-dev r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-snow sbuild-build-depends-genomicalignments-dummy ucf unzip x11-common x11-xkb-utils xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xserver-common xvfb zip zlib1g-dev 0 upgraded, 164 newly installed, 0 to remove and 0 not upgraded. Need to get 81.9 MB/81.9 MB of archives. After this operation, 200 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! r-base-core r-base-dev r-bioc-biocgenerics r-cran-lambda.r r-cran-futile.options r-cran-futile.logger r-bioc-biocparallel r-bioc-s4vectors r-bioc-iranges r-bioc-xvector r-bioc-zlibbioc r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-rsamtools sbuild-build-depends-genomicalignments-dummy Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty-security/main libexpat1 amd64 2.1.0-4ubuntu1.1 [71.1 kB] Get:2 http://ppa.launchpad.net/marutter/rrutter/ubuntu/ trusty/main r-base-core amd64 3.2.2-1trusty0 [20.4 MB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-security/main libmagic1 amd64 1:5.14-2ubuntu3.3 [185 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasprintf0c2 amd64 0.18.3.1-1ubuntu3 [6712 B] Get:5 http://ftpmaster.internal/ubuntu/ trusty-updates/main libglib2.0-0 amd64 2.40.2-0ubuntu1 [1058 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 amd64 1.3.0-1 [24.0 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libxau6 amd64 1:1.0.8-1 [8376 B] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main libxdmcp6 amd64 1:1.1.1-1 [12.8 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main libxcb1 amd64 1.10-2ubuntu1 [38.0 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libx11-data all 2:1.6.2-1ubuntu2 [111 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libx11-6 amd64 2:1.6.2-1ubuntu2 [560 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-security/main libxext6 amd64 2:1.3.2-1ubuntu0.0.14.04.1 [28.8 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty-security/main libxml2 amd64 2.9.1+dfsg1-3ubuntu4.4 [570 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libxmuu1 amd64 2:1.1.1-1 [11.0 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main groff-base amd64 1.22.2-5 [1053 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty-updates/main man-db amd64 2.6.7.1-1ubuntu1 [857 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main fonts-dejavu-core all 2.34-1ubuntu1 [1024 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main ucf all 3.0027+nmu1 [56.3 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-updates/main fontconfig-config all 2.11.0-0ubuntu4.1 [47.4 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-security/main libfreetype6 amd64 2.5.2-1ubuntu2.5 [304 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty-updates/main libfontconfig1 amd64 2.11.0-0ubuntu4.1 [123 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libpixman-1-0 amd64 0.30.2-2ubuntu1 [227 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-render0 amd64 1.10-2ubuntu1 [11.0 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-shm0 amd64 1.10-2ubuntu1 [5432 B] Get:26 http://ftpmaster.internal/ubuntu/ trusty-security/main libxrender1 amd64 1:0.9.8-1build0.14.04.1 [17.9 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty-updates/main libcairo2 amd64 1.13.0~20140204-0ubuntu1.1 [535 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty-security/main libcurl3 amd64 7.35.0-1ubuntu2.5 [173 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main libdatrie1 amd64 0.2.8-1 [16.7 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main libfontenc1 amd64 1:1.1.2-1 [15.6 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgfortran3 amd64 4.8.4-2ubuntu1~14.04 [249 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty-updates/main libglapi-mesa amd64 10.1.3-0ubuntu0.4 [21.4 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main libx11-xcb1 amd64 2:1.6.2-1ubuntu2 [9426 B] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-dri2-0 amd64 1.10-2ubuntu1 [6710 B] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-dri3-0 amd64 1.10-2ubuntu1 [5118 B] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-glx0 amd64 1.10-2ubuntu1 [20.0 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-present0 amd64 1.10-2ubuntu1 [5254 B] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main libxcb-sync1 amd64 1.10-2ubuntu1 [8090 B] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libxdamage1 amd64 1:1.1.4-1ubuntu1 [7612 B] Get:41 http://ftpmaster.internal/ubuntu/ trusty-security/main libxfixes3 amd64 1:5.0.1-1ubuntu1.1 [10.4 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main libxshmfence1 amd64 1.1-2 [4644 B] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main libxxf86vm1 amd64 1:1.1.3-1 [11.7 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgl1-mesa-glx amd64 10.1.3-0ubuntu0.4 [114 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main libgraphite2-3 amd64 1.2.4-1ubuntu1 [53.8 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty-updates/main libharfbuzz0b amd64 0.9.27-1ubuntu1 [127 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty-updates/main x11-common all 1:7.7+1ubuntu8.1 [49.5 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main libice6 amd64 2:1.0.8-2 [47.0 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main libthai-data all 0.1.20-3 [130 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main libthai0 amd64 0.1.20-3 [16.9 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty-updates/main fontconfig amd64 2.11.0-0ubuntu4.1 [176 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpango-1.0-0 amd64 1.36.3-1ubuntu1.1 [149 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpangoft2-1.0-0 amd64 1.36.3-1ubuntu1.1 [32.7 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-updates/main libpangocairo-1.0-0 amd64 1.36.3-1ubuntu1.1 [20.0 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libpaper1 amd64 1.1.24+nmu2ubuntu3 [13.4 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty-security/main libpcrecpp0 amd64 1:8.31-2ubuntu2.1 [14.5 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main libsigsegv2 amd64 2.10-2 [15.0 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main libsm6 amd64 2:1.2.1-2 [18.1 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main libtcl8.6 amd64 8.6.1-4ubuntu1 [841 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty-security/main libjbig0 amd64 2.0-2ubuntu4.1 [26.1 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:63 http://ftpmaster.internal/ubuntu/ trusty-security/main libtiff5 amd64 4.0.3-7ubuntu0.3 [143 kB] Get:64 http://ppa.launchpad.net/marutter/rrutter/ubuntu/ trusty/main r-base-dev all 3.2.2-1trusty0 [4296 B] Get:65 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-biocgenerics all 0.14.0-1cran1ppa0 [436 kB] Get:66 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-cran-lambda.r all 1.1.7-1cran1ppa0 [65.3 kB] Get:67 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-cran-futile.options all 1.0.0-1cran1precise3 [15.4 kB] Get:68 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-cran-futile.logger all 1.4.1-1cran1ppa0 [82.1 kB] Get:69 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-biocparallel all 1.2.9-1cran1ppa0 [623 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty/main libxft2 amd64 2.3.1-2 [36.2 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main libxss1 amd64 1:1.2.2-1 [8582 B] Get:72 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-s4vectors amd64 0.6.5-1cran1ppa0 [753 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main libtk8.6 amd64 8.6.1-3ubuntu2 [689 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:75 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-iranges amd64 2.2.7-2biolinux1 [1523 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty/main libxt6 amd64 1:1.1.4-1 [185 kB] Get:77 http://ftpmaster.internal/ubuntu/ trusty/main libxmu6 amd64 2:1.1.1-1 [53.8 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty/main libxpm4 amd64 1:3.5.10-1 [38.3 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty/main libxaw7 amd64 2:1.0.12-1 [168 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty-security/main libxfont1 amd64 1:1.4.7-1ubuntu0.2 [95.0 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty/main libxkbfile1 amd64 1:1.0.8-1 [74.2 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty-security/main libpython2.7-minimal amd64 2.7.6-8ubuntu0.2 [308 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty-security/main python2.7-minimal amd64 2.7.6-8ubuntu0.2 [1185 kB] Get:84 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-xvector amd64 0.8.0-2biolinux2 [326 kB] Get:85 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-zlibbioc amd64 1.10.0-0biolinux1 [105 kB] Get:86 http://ftpmaster.internal/ubuntu/ trusty-security/main file amd64 1:5.14-2ubuntu3.3 [18.9 kB] Get:87 http://ftpmaster.internal/ubuntu/ trusty-security/main mime-support all 3.54ubuntu1.1 [29.3 kB] Get:88 http://ftpmaster.internal/ubuntu/ trusty/main netbase all 5.2 [12.9 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty/main xkb-data all 2.10.1-1ubuntu1 [294 kB] Get:90 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-biostrings amd64 2.36.4-2biolinux1 [13.5 MB] Get:91 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext-base amd64 0.18.3.1-1ubuntu3 [48.8 kB] Get:92 http://ftpmaster.internal/ubuntu/ trusty/main xauth amd64 1:1.0.7-1ubuntu1 [25.8 kB] Get:93 http://ftpmaster.internal/ubuntu/ trusty/main m4 amd64 1.4.17-2ubuntu1 [195 kB] Get:94 http://ftpmaster.internal/ubuntu/ trusty/main autoconf all 2.69-6 [322 kB] Get:95 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:96 http://ftpmaster.internal/ubuntu/ trusty/main automake all 1:1.14.1-2ubuntu1 [510 kB] Get:97 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext amd64 0.18.3.1-1ubuntu3 [829 kB] Get:98 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:99 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:100 http://ftpmaster.internal/ubuntu/ trusty-updates/main dh-apparmor all 2.8.95~2430-0ubuntu5.3 [12.2 kB] Get:101 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:102 http://ftpmaster.internal/ubuntu/ trusty/main liburi-perl all 1.60-1 [89.6 kB] Get:103 http://ftpmaster.internal/ubuntu/ trusty/main libencode-locale-perl all 1.03-1 [12.4 kB] Get:104 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-date-perl all 6.02-1 [10.4 kB] Get:105 http://ftpmaster.internal/ubuntu/ trusty/main libfile-listing-perl all 6.04-1 [9774 B] Get:106 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:107 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-parser-perl amd64 3.71-1build1 [98.2 kB] Get:108 http://ftpmaster.internal/ubuntu/ trusty/main libhtml-tree-perl all 5.03-1 [215 kB] Get:109 http://ftpmaster.internal/ubuntu/ trusty/main libio-html-perl all 1.00-1 [15.7 kB] Get:110 http://ftpmaster.internal/ubuntu/ trusty/main liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:111 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-message-perl all 6.06-1 [78.7 kB] Get:112 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-cookies-perl all 6.00-2 [23.3 kB] Get:113 http://ftpmaster.internal/ubuntu/ trusty/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:114 http://ftpmaster.internal/ubuntu/ trusty/main libnet-ssleay-perl amd64 1.58-1 [243 kB] Get:115 http://ftpmaster.internal/ubuntu/ trusty/main libio-socket-ssl-perl all 1.965-1ubuntu1 [73.7 kB] Get:116 http://ftpmaster.internal/ubuntu/ trusty/main libnet-http-perl all 6.06-1 [24.2 kB] Get:117 http://ftpmaster.internal/ubuntu/ trusty-security/main liblwp-protocol-https-perl all 6.04-2ubuntu0.1 [7644 B] Get:118 http://ftpmaster.internal/ubuntu/ trusty/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:119 http://ftpmaster.internal/ubuntu/ trusty/main libwww-perl all 6.05-2 [146 kB] Get:120 http://ftpmaster.internal/ubuntu/ trusty/main libxml-parser-perl amd64 2.41-1build3 [294 kB] Get:121 http://ftpmaster.internal/ubuntu/ trusty/main intltool all 0.50.2-2 [52.0 kB] Get:122 http://ftpmaster.internal/ubuntu/ trusty/main dh-translations all 121 [21.6 kB] Get:123 http://ftpmaster.internal/ubuntu/ trusty-security/main libpython2.7-stdlib amd64 2.7.6-8ubuntu0.2 [1869 kB] Get:124 http://ftpmaster.internal/ubuntu/ trusty-security/main python2.7 amd64 2.7.6-8ubuntu0.2 [196 kB] Get:125 http://ftpmaster.internal/ubuntu/ trusty/main python-minimal amd64 2.7.5-5ubuntu3 [27.5 kB] Get:126 http://ftpmaster.internal/ubuntu/ trusty/main libpython-stdlib amd64 2.7.5-5ubuntu3 [7012 B] Get:127 http://ftpmaster.internal/ubuntu/ trusty/main python amd64 2.7.5-5ubuntu3 [134 kB] Get:128 http://ftpmaster.internal/ubuntu/ trusty/main python-scour all 0.26-3build1 [40.5 kB] Get:129 http://ftpmaster.internal/ubuntu/ trusty/main cdbs all 0.4.122ubuntu2 [42.1 kB] Get:130 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgfortran-4.8-dev amd64 4.8.4-2ubuntu1~14.04 [269 kB] Get:131 http://ftpmaster.internal/ubuntu/ trusty-updates/main gfortran-4.8 amd64 4.8.4-2ubuntu1~14.04 [4881 kB] Get:132 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-genomeinfodb all 1.4.2-1cran1ppa0 [430 kB] Get:133 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-genomicranges amd64 1.20.6-2biolinux2 [1431 kB] Get:134 http://ftpmaster.internal/ubuntu/ trusty/main gfortran amd64 4:4.8.2-1ubuntu6 [1252 B] Get:135 http://ftpmaster.internal/ubuntu/ trusty/main libblas3 amd64 1.2.20110419-7 [215 kB] Get:136 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main r-bioc-rsamtools amd64 1.20.4-2biolinux3 [3209 kB] Get:137 http://ftpmaster.internal/ubuntu/ trusty/main libblas-dev amd64 1.2.20110419-7 [240 kB] Get:138 http://ftpmaster.internal/ubuntu/ trusty/main libbz2-dev amd64 1.0.6-5 [33.2 kB] Get:139 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg-turbo8-dev amd64 1.3.0-0ubuntu2 [242 kB] Get:140 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:141 http://ftpmaster.internal/ubuntu/ trusty/main libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:142 http://ftpmaster.internal/ubuntu/ trusty/main liblapack3 amd64 3.5.0-2ubuntu1 [1730 kB] Get:143 http://ftpmaster.internal/ubuntu/ trusty/main liblapack-dev amd64 3.5.0-2ubuntu1 [1740 kB] Get:144 http://ftpmaster.internal/ubuntu/ trusty/main libtinfo-dev amd64 5.9+20140118-1ubuntu1 [76.3 kB] Get:145 http://ftpmaster.internal/ubuntu/ trusty/main libncurses5-dev amd64 5.9+20140118-1ubuntu1 [170 kB] Get:146 http://ftpmaster.internal/ubuntu/ trusty/main libpaper-utils amd64 1.1.24+nmu2ubuntu3 [8244 B] Get:147 http://ftpmaster.internal/ubuntu/ trusty-security/main libpcre3-dev amd64 1:8.31-2ubuntu2.1 [237 kB] Get:148 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] Get:149 http://ftpmaster.internal/ubuntu/ trusty/main libpng12-dev amd64 1.2.50-1ubuntu2 [206 kB] Get:150 http://ftpmaster.internal/ubuntu/ trusty/main libreadline6-dev amd64 6.3-4ubuntu2 [213 kB] Get:151 http://ftpmaster.internal/ubuntu/ trusty/main libreadline-dev amd64 6.3-4ubuntu2 [988 B] Get:152 http://ftpmaster.internal/ubuntu/ trusty/main zip amd64 3.0-8 [262 kB] Get:153 http://ftpmaster.internal/ubuntu/ trusty-security/main unzip amd64 6.0-9ubuntu1.3 [157 kB] Get:154 http://ftpmaster.internal/ubuntu/ trusty-updates/main xdg-utils all 1.1.0~rc1-2ubuntu7.1 [54.1 kB] Get:155 http://ftpmaster.internal/ubuntu/ trusty/main liblzma-dev amd64 5.1.1alpha+20120614-2ubuntu2 [137 kB] Get:156 http://ftpmaster.internal/ubuntu/ trusty/universe r-cran-snow all 1:0.3.13-1 [67.9 kB] Get:157 http://ftpmaster.internal/ubuntu/ trusty/universe r-cran-bitops amd64 1.0-6-1 [23.4 kB] Get:158 http://ftpmaster.internal/ubuntu/ trusty/main x11-xkb-utils amd64 7.7+1 [156 kB] Get:159 http://ftpmaster.internal/ubuntu/ trusty/main xfonts-encodings all 1:1.0.4-1ubuntu1 [583 kB] Get:160 http://ftpmaster.internal/ubuntu/ trusty/main xfonts-utils amd64 1:7.7+1 [73.9 kB] Get:161 http://ftpmaster.internal/ubuntu/ trusty/main xfonts-base all 1:1.0.3 [6180 kB] Get:162 http://ftpmaster.internal/ubuntu/ trusty-security/main xserver-common all 2:1.15.1-0ubuntu2.7 [27.9 kB] Get:163 http://ftpmaster.internal/ubuntu/ trusty-security/main xvfb amd64 2:1.15.1-0ubuntu2.7 [747 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 81.9 MB in 5s (15.1 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 11837 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1.1_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-4ubuntu1.1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu3.3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.14-2ubuntu3.3) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu3_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.18.3.1-1ubuntu3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.40.2-0ubuntu1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.40.2-0ubuntu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package libxau6:amd64. 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Unpacking libxcb-render0:amd64 (1.10-2ubuntu1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../libxcb-shm0_1.10-2ubuntu1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.10-2ubuntu1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../libxrender1_1%3a0.9.8-1build0.14.04.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.8-1build0.14.04.1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../libcairo2_1.13.0~20140204-0ubuntu1.1_amd64.deb ... Unpacking libcairo2:amd64 (1.13.0~20140204-0ubuntu1.1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-2ubuntu1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-2ubuntu1) ... Selecting previously unselected package libcurl3:amd64. Preparing to unpack .../libcurl3_7.35.0-1ubuntu2.5_amd64.deb ... Unpacking libcurl3:amd64 (7.35.0-1ubuntu2.5) ... 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Unpacking xfonts-base (1:1.0.3) ... Selecting previously unselected package xserver-common. Preparing to unpack .../xserver-common_2%3a1.15.1-0ubuntu2.7_all.deb ... Unpacking xserver-common (2:1.15.1-0ubuntu2.7) ... Selecting previously unselected package xvfb. Preparing to unpack .../xvfb_2%3a1.15.1-0ubuntu2.7_amd64.deb ... Unpacking xvfb (2:1.15.1-0ubuntu2.7) ... Selecting previously unselected package sbuild-build-depends-genomicalignments-dummy. Preparing to unpack .../sbuild-build-depends-genomicalignments-dummy.deb ... Unpacking sbuild-build-depends-genomicalignments-dummy (0.invalid.0) ... Setting up libexpat1:amd64 (2.1.0-4ubuntu1.1) ... Setting up libmagic1:amd64 (1:5.14-2ubuntu3.3) ... Setting up libasprintf0c2:amd64 (0.18.3.1-1ubuntu3) ... Setting up libglib2.0-0:amd64 (2.40.2-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.10-2ubuntu1) ... Setting up libx11-data (2:1.6.2-1ubuntu2) ... Setting up libx11-6:amd64 (2:1.6.2-1ubuntu2) ... Setting up libxext6:amd64 (2:1.3.2-1ubuntu0.0.14.04.1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3ubuntu4.4) ... Setting up libxmuu1:amd64 (2:1.1.1-1) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.7.1-1ubuntu1) ... Not building database; man-db/auto-update is not 'true'. Setting up fonts-dejavu-core (2.34-1ubuntu1) ... Setting up ucf (3.0027+nmu1) ... Setting up fontconfig-config (2.11.0-0ubuntu4.1) ... Setting up libfreetype6:amd64 (2.5.2-1ubuntu2.5) ... Setting up libfontconfig1:amd64 (2.11.0-0ubuntu4.1) ... Setting up libpixman-1-0:amd64 (0.30.2-2ubuntu1) ... Setting up libxcb-render0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-shm0:amd64 (1.10-2ubuntu1) ... Setting up libxrender1:amd64 (1:0.9.8-1build0.14.04.1) ... Setting up libcairo2:amd64 (1.13.0~20140204-0ubuntu1.1) ... Setting up libcroco3:amd64 (0.6.8-2ubuntu1) ... Setting up libcurl3:amd64 (7.35.0-1ubuntu2.5) ... Setting up libdatrie1:amd64 (0.2.8-1) ... Setting up libfontenc1:amd64 (1:1.1.2-1) ... Setting up libgfortran3:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up libglapi-mesa:amd64 (10.1.3-0ubuntu0.4) ... Setting up libx11-xcb1:amd64 (2:1.6.2-1ubuntu2) ... Setting up libxcb-dri2-0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-dri3-0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-glx0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-present0:amd64 (1.10-2ubuntu1) ... Setting up libxcb-sync1:amd64 (1.10-2ubuntu1) ... Setting up libxdamage1:amd64 (1:1.1.4-1ubuntu1) ... Setting up libxfixes3:amd64 (1:5.0.1-1ubuntu1.1) ... Setting up libxshmfence1:amd64 (1.1-2) ... Setting up libxxf86vm1:amd64 (1:1.1.3-1) ... Setting up libgl1-mesa-glx:amd64 (10.1.3-0ubuntu0.4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf (x86_64-linux-gnu_gl_conf) in auto mode Setting up libgraphite2-3:amd64 (1.2.4-1ubuntu1) ... Setting up libharfbuzz0b:amd64 (0.9.27-1ubuntu1) ... Setting up x11-common (1:7.7+1ubuntu8.1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:amd64 (2:1.0.8-2) ... Setting up libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ... Setting up libthai-data (0.1.20-3) ... Setting up libthai0:amd64 (0.1.20-3) ... Setting up fontconfig (2.11.0-0ubuntu4.1) ... Regenerating fonts cache... done. Setting up libpango-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libpangoft2-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libpangocairo-1.0-0:amd64 (1.36.3-1ubuntu1.1) ... Setting up libpaper1:amd64 (1.1.24+nmu2ubuntu3) ... Creating config file /etc/papersize with new version Setting up libpcrecpp0:amd64 (1:8.31-2ubuntu2.1) ... Setting up libsigsegv2:amd64 (2.10-2) ... Setting up libsm6:amd64 (2:1.2.1-2) ... Setting up libtcl8.6:amd64 (8.6.1-4ubuntu1) ... Setting up libjbig0:amd64 (2.0-2ubuntu4.1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libtiff5:amd64 (4.0.3-7ubuntu0.3) ... Setting up libxft2:amd64 (2.3.1-2) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libtk8.6:amd64 (8.6.1-3ubuntu2) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... Setting up libxt6:amd64 (1:1.1.4-1) ... Setting up libxmu6:amd64 (2:1.1.1-1) ... Setting up libxpm4:amd64 (1:3.5.10-1) ... Setting up libxaw7:amd64 (2:1.0.12-1) ... Setting up libxfont1:amd64 (1:1.4.7-1ubuntu0.2) ... Setting up libxkbfile1:amd64 (1:1.0.8-1) ... Setting up libpython2.7-minimal:amd64 (2.7.6-8ubuntu0.2) ... Setting up python2.7-minimal (2.7.6-8ubuntu0.2) ... Setting up file (1:5.14-2ubuntu3.3) ... Setting up mime-support (3.54ubuntu1.1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up netbase (5.2) ... Setting up xkb-data (2.10.1-1ubuntu1) ... Setting up gettext-base (0.18.3.1-1ubuntu3) ... Setting up xauth (1:1.0.7-1ubuntu1) ... Setting up m4 (1.4.17-2ubuntu1) ... Setting up autoconf (2.69-6) ... Setting up autotools-dev (20130810.1) ... Setting up automake (1:1.14.1-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.18.3.1-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.8.95~2430-0ubuntu5.3) ... Setting up debhelper (9.20131227ubuntu1) ... Setting up liburi-perl (1.60-1) ... Setting up libencode-locale-perl (1.03-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.71-1build1) ... Setting up libhtml-tree-perl (5.03-1) ... Setting up libio-html-perl (1.00-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.06-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.58-1) ... Setting up libio-socket-ssl-perl (1.965-1ubuntu1) ... Setting up libnet-http-perl (6.06-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.6-8ubuntu0.2) ... Setting up python2.7 (2.7.6-8ubuntu0.2) ... Setting up python-minimal (2.7.5-5ubuntu3) ... Setting up libpython-stdlib:amd64 (2.7.5-5ubuntu3) ... Setting up python (2.7.5-5ubuntu3) ... Setting up python-scour (0.26-3build1) ... Setting up libgfortran-4.8-dev:amd64 (4.8.4-2ubuntu1~14.04) ... Setting up gfortran-4.8 (4.8.4-2ubuntu1~14.04) ... Setting up gfortran (4:4.8.2-1ubuntu6) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode Setting up libblas3 (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas-dev (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libbz2-dev:amd64 (1.0.6-5) ... Setting up libjpeg-turbo8-dev:amd64 (1.3.0-0ubuntu2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up liblapack3 (3.5.0-2ubuntu1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.5.0-2ubuntu1) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libtinfo-dev:amd64 (5.9+20140118-1ubuntu1) ... Setting up libncurses5-dev:amd64 (5.9+20140118-1ubuntu1) ... Setting up libpaper-utils (1.1.24+nmu2ubuntu3) ... Setting up libpcre3-dev:amd64 (1:8.31-2ubuntu2.1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... Setting up libpng12-dev (1.2.50-1ubuntu2) ... Setting up libreadline6-dev:amd64 (6.3-4ubuntu2) ... Setting up libreadline-dev:amd64 (6.3-4ubuntu2) ... Setting up zip (3.0-8) ... Setting up unzip (6.0-9ubuntu1.3) ... Setting up xdg-utils (1.1.0~rc1-2ubuntu7.1) ... Setting up r-base-core (3.2.2-1trusty0) ... Creating config file /etc/R/Renviron with new version Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2ubuntu2) ... Setting up r-bioc-biocgenerics (0.14.0-1cran1ppa0) ... Setting up r-cran-lambda.r (1.1.7-1cran1ppa0) ... Setting up r-cran-futile.options (1.0.0-1cran1precise3) ... Setting up r-cran-futile.logger (1.4.1-1cran1ppa0) ... Setting up r-cran-snow (1:0.3.13-1) ... Setting up r-bioc-biocparallel (1.2.9-1cran1ppa0) ... Setting up r-bioc-s4vectors (0.6.5-1cran1ppa0) ... Setting up r-bioc-iranges (2.2.7-2biolinux1) ... Setting up r-bioc-xvector (0.8.0-2biolinux2) ... Setting up r-bioc-zlibbioc (1.10.0-0biolinux1) ... Setting up r-bioc-biostrings (2.36.4-2biolinux1) ... Setting up r-bioc-genomeinfodb (1.4.2-1cran1ppa0) ... Setting up r-bioc-genomicranges (1.20.6-2biolinux2) ... Setting up r-cran-bitops (1.0-6-1) ... Setting up r-bioc-rsamtools (1.20.4-2biolinux3) ... Setting up x11-xkb-utils (7.7+1) ... Setting up xfonts-encodings (1:1.0.4-1ubuntu1) ... Setting up xfonts-utils (1:7.7+1) ... Setting up xfonts-base (1:1.0.3) ... Setting up xserver-common (2:1.15.1-0ubuntu2.7) ... Setting up xvfb (2:1.15.1-0ubuntu2.7) ... Setting up liblwp-protocol-https-perl (6.04-2ubuntu0.1) ... Setting up libwww-perl (6.05-2) ... Setting up libxml-parser-perl (2.41-1build3) ... Setting up intltool (0.50.2-2) ... Setting up dh-translations (121) ... Setting up cdbs (0.4.122ubuntu2) ... Setting up r-base-dev (3.2.2-1trusty0) ... Setting up sbuild-build-depends-genomicalignments-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-0ubuntu6.6) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-28-generic amd64 (x86_64) Toolchain package versions: binutils_2.24-5ubuntu13 dpkg-dev_1.17.5ubuntu5.4 g++-4.8_4.8.4-2ubuntu1~14.04 gcc-4.8_4.8.4-2ubuntu1~14.04 libc6-dev_2.19-0ubuntu6.6 libstdc++-4.8-dev_4.8.4-2ubuntu1~14.04 libstdc++6_4.8.4-2ubuntu1~14.04 linux-libc-dev_3.13.0-63.103 Package versions: adduser_3.113+nmu3ubuntu3 advancecomp_1.18-1 apt_1.0.1ubuntu2.10 apt-transport-https_1.0.1ubuntu2.10 autoconf_2.69-6 automake_1:1.14.1-2ubuntu1 autotools-dev_20130810.1 base-files_7.2ubuntu5.3 base-passwd_3.5.33 bash_4.3-7ubuntu1.5 binutils_2.24-5ubuntu13 bsdmainutils_9.0.5ubuntu1 bsdutils_1:2.20.1-5.1ubuntu20.6 build-essential_11.6ubuntu6 busybox-initramfs_1:1.21.0-1ubuntu1 bzip2_1.0.6-5 ca-certificates_20141019ubuntu0.14.04.1 cdbs_0.4.122ubuntu2 coreutils_8.21-1ubuntu5.1 cpio_2.11+dfsg-1ubuntu1.1 cpp_4:4.8.2-1ubuntu6 cpp-4.8_4.8.4-2ubuntu1~14.04 dash_0.5.7-4ubuntu1 debconf_1.5.51ubuntu2 debhelper_9.20131227ubuntu1 debianutils_4.4 dh-apparmor_2.8.95~2430-0ubuntu5.3 dh-translations_121 diffutils_1:3.3-1 dpkg_1.17.5ubuntu5.4 dpkg-dev_1.17.5ubuntu5.4 e2fslibs_1.42.9-3ubuntu1.2 e2fsprogs_1.42.9-3ubuntu1.2 fakeroot_1.20-3ubuntu2 file_1:5.14-2ubuntu3.3 findutils_4.4.2-7 fontconfig_2.11.0-0ubuntu4.1 fontconfig-config_2.11.0-0ubuntu4.1 fonts-dejavu-core_2.34-1ubuntu1 g++_4:4.8.2-1ubuntu6 g++-4.8_4.8.4-2ubuntu1~14.04 gcc_4:4.8.2-1ubuntu6 gcc-4.8_4.8.4-2ubuntu1~14.04 gcc-4.8-base_4.8.4-2ubuntu1~14.04 gcc-4.9-base_4.9.1-0ubuntu1 gettext_0.18.3.1-1ubuntu3 gettext-base_0.18.3.1-1ubuntu3 gfortran_4:4.8.2-1ubuntu6 gfortran-4.8_4.8.4-2ubuntu1~14.04 gnupg_1.4.16-1ubuntu2.3 gpgv_1.4.16-1ubuntu2.3 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3ubuntu1 hostname_3.15ubuntu1 ifupdown_0.7.47.2ubuntu4.1 initramfs-tools_0.103ubuntu4.2 initramfs-tools-bin_0.103ubuntu4.2 initscripts_2.88dsf-41ubuntu6.2 insserv_1.14.0-5ubuntu2 intltool_0.50.2-2 intltool-debian_0.35.0+20060710.1 iproute2_3.12.0-2ubuntu1 klibc-utils_2.0.3-0ubuntu1 kmod_15-0ubuntu6 libacl1_2.2.52-1 libapt-pkg4.12_1.0.1ubuntu2.10 libasan0_4.8.4-2ubuntu1~14.04 libasn1-8-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libasprintf0c2_0.18.3.1-1ubuntu3 libatomic1_4.8.4-2ubuntu1~14.04 libattr1_1:2.4.47-1ubuntu1 libaudit-common_1:2.3.2-2ubuntu1 libaudit1_1:2.3.2-2ubuntu1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.1ubuntu20.6 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.19-0ubuntu6.6 libc-dev-bin_2.19-0ubuntu6.6 libc6_2.19-0ubuntu6.6 libc6-dev_2.19-0ubuntu6.6 libcairo2_1.13.0~20140204-0ubuntu1.1 libcap2_1:2.24-0ubuntu2 libcgmanager0_0.24-0ubuntu7.3 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3ubuntu1.2 libcroco3_0.6.8-2ubuntu1 libcurl3_7.35.0-1ubuntu2.5 libcurl3-gnutls_7.35.0-1ubuntu2.5 libdatrie1_0.2.8-1 libdb5.3_5.3.28-3ubuntu3 libdbus-1-3_1.6.18-0ubuntu4.3 libdebconfclient0_0.187ubuntu1 libdpkg-perl_1.17.5ubuntu5.4 libdrm2_2.4.60-2~ubuntu14.04.1 libencode-locale-perl_1.03-1 libexpat1_2.1.0-4ubuntu1.1 libfakeroot_1.20-3ubuntu2 libffi6_3.1~rc1+r3.0.13-12 libfile-listing-perl_6.04-1 libfontconfig1_2.11.0-0ubuntu4.1 libfontenc1_1:1.1.2-1 libfreetype6_2.5.2-1ubuntu2.5 libgcc-4.8-dev_4.8.4-2ubuntu1~14.04 libgcc1_1:4.9.1-0ubuntu1 libgcrypt11_1.5.3-2ubuntu4.2 libgdbm3_1.8.3-12build1 libgfortran-4.8-dev_4.8.4-2ubuntu1~14.04 libgfortran3_4.8.4-2ubuntu1~14.04 libgl1-mesa-glx_10.1.3-0ubuntu0.4 libglapi-mesa_10.1.3-0ubuntu0.4 libglib2.0-0_2.40.2-0ubuntu1 libgmp10_2:5.1.3+dfsg-1ubuntu1 libgnutls26_2.12.23-12ubuntu2.2 libgomp1_4.8.4-2ubuntu1~14.04 libgpg-error0_1.12-0.2ubuntu1 libgraphite2-3_1.2.4-1ubuntu1 libgssapi-krb5-2_1.12+dfsg-2ubuntu5.1 libgssapi3-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libharfbuzz0b_0.9.27-1ubuntu1 libhcrypto4-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimbase1-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimntlm0-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libhtml-parser-perl_3.71-1build1 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_5.03-1 libhttp-cookies-perl_6.00-2 libhttp-date-perl_6.02-1 libhttp-message-perl_6.06-1 libhttp-negotiate-perl_6.00-2 libhx509-5-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libice6_2:1.0.8-2 libidn11_1.28-1ubuntu2 libio-html-perl_1.00-1 libio-socket-ssl-perl_1.965-1ubuntu1 libisl10_0.12.2-1 libitm1_4.8.4-2ubuntu1~14.04 libjbig0_2.0-2ubuntu4.1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_1.3.0-0ubuntu2 libjpeg-turbo8-dev_1.3.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c2_0.11-3ubuntu1.2 libjson0_0.11-3ubuntu1.2 libk5crypto3_1.12+dfsg-2ubuntu5.1 libkeyutils1_1.5.6-1 libklibc_2.0.3-0ubuntu1 libkmod2_15-0ubuntu6 libkrb5-26-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libkrb5-3_1.12+dfsg-2ubuntu5.1 libkrb5support0_1.12+dfsg-2ubuntu5.1 liblapack-dev_3.5.0-2ubuntu1 liblapack3_3.5.0-2ubuntu1 libldap-2.4-2_2.4.31-1+nmu2ubuntu8.1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.04-2ubuntu0.1 liblzma-dev_5.1.1alpha+20120614-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.14-2ubuntu3.3 libmount1_2.20.1-5.1ubuntu20.6 libmpc3_1.0.1-1ubuntu1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1ubuntu1 libncurses5-dev_5.9+20140118-1ubuntu1 libncursesw5_5.9+20140118-1ubuntu1 libnet-http-perl_6.06-1 libnet-ssleay-perl_1.58-1 libnih-dbus1_1.0.3-4ubuntu25 libnih1_1.0.3-4ubuntu25 libp11-kit0_0.20.2-2ubuntu2 libpam-modules_1.1.8-1ubuntu2 libpam-modules-bin_1.1.8-1ubuntu2 libpam-runtime_1.1.8-1ubuntu2 libpam0g_1.1.8-1ubuntu2 libpango-1.0-0_1.36.3-1ubuntu1.1 libpangocairo-1.0-0_1.36.3-1ubuntu1.1 libpangoft2-1.0-0_1.36.3-1ubuntu1.1 libpaper-utils_1.1.24+nmu2ubuntu3 libpaper1_1.1.24+nmu2ubuntu3 libpcre3_1:8.31-2ubuntu2.1 libpcre3-dev_1:8.31-2ubuntu2.1 libpcrecpp0_1:8.31-2ubuntu2.1 libpipeline1_1.3.0-1 libpixman-1-0_0.30.2-2ubuntu1 libplymouth2_0.8.8-0ubuntu17.1 libpng12-0_1.2.50-1ubuntu2 libpng12-dev_1.2.50-1ubuntu2 libprocps3_1:3.3.9-1ubuntu2.2 libpython-stdlib_2.7.5-5ubuntu3 libpython2.7-minimal_2.7.6-8ubuntu0.2 libpython2.7-stdlib_2.7.6-8ubuntu0.2 libquadmath0_4.8.4-2ubuntu1~14.04 libreadline-dev_6.3-4ubuntu2 libreadline6_6.3-4ubuntu2 libreadline6-dev_6.3-4ubuntu2 libroken18-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 librtmp0_2.4+20121230.gitdf6c518-1 libsasl2-2_2.1.25.dfsg1-17build1 libsasl2-modules-db_2.1.25.dfsg1-17build1 libselinux1_2.2.2-1ubuntu0.1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1ubuntu0.1 libsigsegv2_2.10-2 libslang2_2.2.4-15ubuntu1 libsm6_2:1.2.1-2 libsqlite3-0_3.8.2-1ubuntu2.1 libss2_1.42.9-3ubuntu1.2 libssl1.0.0_1.0.1f-1ubuntu2.15 libstdc++-4.8-dev_4.8.4-2ubuntu1~14.04 libstdc++6_4.8.4-2ubuntu1~14.04 libtasn1-6_3.4-3ubuntu0.3 libtcl8.6_8.6.1-4ubuntu1 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-7ubuntu0.3 libtimedate-perl_2.3000-1 libtinfo-dev_5.9+20140118-1ubuntu1 libtinfo5_5.9+20140118-1ubuntu1 libtk8.6_8.6.1-3ubuntu2 libtsan0_4.8.4-2ubuntu1~14.04 libudev1_204-5ubuntu20.13 libunistring0_0.9.3-5ubuntu3 liburi-perl_1.60-1 libusb-0.1-4_2:0.1.12-23.3ubuntu1 libustr-1.0-1_1.0.4-3ubuntu2 libuuid1_2.20.1-5.1ubuntu20.6 libwind0-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libwww-perl_6.05-2 libwww-robotrules-perl_6.01-1 libx11-6_2:1.6.2-1ubuntu2 libx11-data_2:1.6.2-1ubuntu2 libx11-xcb1_2:1.6.2-1ubuntu2 libxau6_1:1.0.8-1 libxaw7_2:1.0.12-1 libxcb-dri2-0_1.10-2ubuntu1 libxcb-dri3-0_1.10-2ubuntu1 libxcb-glx0_1.10-2ubuntu1 libxcb-present0_1.10-2ubuntu1 libxcb-render0_1.10-2ubuntu1 libxcb-shm0_1.10-2ubuntu1 libxcb-sync1_1.10-2ubuntu1 libxcb1_1.10-2ubuntu1 libxdamage1_1:1.1.4-1ubuntu1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1ubuntu0.0.14.04.1 libxfixes3_1:5.0.1-1ubuntu1.1 libxfont1_1:1.4.7-1ubuntu0.2 libxft2_2.3.1-2 libxkbfile1_1:1.0.8-1 libxml-parser-perl_2.41-1build3 libxml2_2.9.1+dfsg1-3ubuntu4.4 libxmu6_2:1.1.1-1 libxmuu1_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender1_1:0.9.8-1build0.14.04.1 libxshmfence1_1.1-2 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.13.0-63.103 lockfile-progs_0.1.17 login_1:4.1.5.1-1ubuntu9.1 lsb-base_4.1+Debian11ubuntu6 m4_1.4.17-2ubuntu1 make_3.81-8.2ubuntu3 makedev_2.3.1-93ubuntu1 man-db_2.6.7.1-1ubuntu1 mawk_1.3.3-17ubuntu2 mime-support_3.54ubuntu1.1 module-init-tools_15-0ubuntu6 mount_2.20.1-5.1ubuntu20.6 mountall_2.53 multiarch-support_2.19-0ubuntu6.6 ncurses-base_5.9+20140118-1ubuntu1 ncurses-bin_5.9+20140118-1ubuntu1 netbase_5.2 openssl_1.0.1f-1ubuntu2.15 optipng_0.6.4-1build1 passwd_1:4.1.5.1-1ubuntu9.1 patch_2.7.1-4ubuntu2.3 perl_5.18.2-2ubuntu1 perl-base_5.18.2-2ubuntu1 perl-modules_5.18.2-2ubuntu1 pkg-create-dbgsym_0.67~trusty pkgbinarymangler_121 plymouth_0.8.8-0ubuntu17.1 po-debconf_1.0.16+nmu2ubuntu1 policyrcd-script-zg2_0.1-2 procps_1:3.3.9-1ubuntu2.2 python_2.7.5-5ubuntu3 python-minimal_2.7.5-5ubuntu3 python-scour_0.26-3build1 python2.7_2.7.6-8ubuntu0.2 python2.7-minimal_2.7.6-8ubuntu0.2 r-base-core_3.2.2-1trusty0 r-base-dev_3.2.2-1trusty0 r-bioc-biocgenerics_0.14.0-1cran1ppa0 r-bioc-biocparallel_1.2.9-1cran1ppa0 r-bioc-biostrings_2.36.4-2biolinux1 r-bioc-genomeinfodb_1.4.2-1cran1ppa0 r-bioc-genomicranges_1.20.6-2biolinux2 r-bioc-iranges_2.2.7-2biolinux1 r-bioc-rsamtools_1.20.4-2biolinux3 r-bioc-s4vectors_0.6.5-1cran1ppa0 r-bioc-xvector_0.8.0-2biolinux2 r-bioc-zlibbioc_1.10.0-0biolinux1 r-cran-bitops_1.0-6-1 r-cran-futile.logger_1.4.1-1cran1ppa0 r-cran-futile.options_1.0.0-1cran1precise3 r-cran-lambda.r_1.1.7-1cran1ppa0 r-cran-snow_1:0.3.13-1 readline-common_6.3-4ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genomicalignments-dummy_0.invalid.0 sed_4.2.2-4ubuntu1 sensible-utils_0.0.9 sysv-rc_2.88dsf-41ubuntu6.2 sysvinit-utils_2.88dsf-41ubuntu6.2 tar_1.27.1-1 tzdata_2015f-0ubuntu0.14.04 ubuntu-keyring_2012.05.19 ucf_3.0027+nmu1 udev_204-5ubuntu20.13 unzip_6.0-9ubuntu1.3 upstart_1.12.1-0ubuntu4.2 util-linux_2.20.1-5.1ubuntu20.6 x11-common_1:7.7+1ubuntu8.1 x11-xkb-utils_7.7+1 xauth_1:1.0.7-1ubuntu1 xdg-utils_1.1.0~rc1-2ubuntu7.1 xfonts-base_1:1.0.3 xfonts-encodings_1:1.0.4-1ubuntu1 xfonts-utils_1:7.7+1 xkb-data_2.10.1-1ubuntu1 xserver-common_2:1.15.1-0ubuntu2.7 xvfb_2:1.15.1-0ubuntu2.7 xz-utils_5.1.1alpha+20120614-2ubuntu2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1ubuntu1 zlib1g-dev_1:1.2.8.dfsg-1ubuntu1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Mon May 11 21:39:29 2015 UTC using RSA key ID E084DAB9 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./genomicalignments_1.4.1-1cran1ppa0.dsc dpkg-source: info: extracting genomicalignments in genomicalignments-1.4.1 dpkg-source: info: unpacking genomicalignments_1.4.1.orig.tar.gz dpkg-source: info: applying genomicalignments_1.4.1-1cran1ppa0.diff.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package genomicalignments dpkg-buildpackage: source version 1.4.1-1cran1ppa0 dpkg-buildpackage: source distribution trusty dpkg-source --before-build genomicalignments-1.4.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ "reverse-patches" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: if [ "reverse-patches" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "reverse-patches" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi for dir in debian/patches ; do \ rm -f $dir/*.log ; \ done dh_clean dh_clean: No compatibility level specified in debian/compat dh_clean: This package will soon FTBFS; time to fix it! dh_clean: Compatibility levels before 5 are deprecated (level 1 in use) if test -d src; then \ find src -regex ".*\.o" | \ xargs --no-run-if-empty -r rm; \ fi rm -f config.log config.status debian/rules build-arch /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules mkdir -p "." echo 5 >debian/compat /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ "debian/stamp-patched" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: if [ "debian/stamp-patched" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "debian/stamp-patched" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules dh_testroot dh_clean -k dh_clean: dh_clean -k is deprecated; use dh_prep instead dh_installdirs -A mkdir -p "." dh_installdirs usr/lib/R/site-library echo "R:Depends=r-base-core (>= 3.2.2-1trusty0), r-api-3" >> debian/r-bioc-genomicalignments.substvars if test -f /usr/bin/xvfb-run; then \ xvfb-run -a \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean \ . \ "--built-timestamp=\"Mon, 11 May 2015 21:39:23 +0000\"" \ ; \ else \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library \ --clean . \ "--built-timestamp=\"Mon, 11 May 2015 21:39:23 +0000\"" \ ; \ fi * installing *source* package 'GenomicAlignments' ... ** libs make[1]: Entering directory `/«PKGBUILDDIR»/src' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cigar_utils.c -o cigar_utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Entering directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»/src' installing to /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments/libs ** R ** inst ** preparing package for lazy loading Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' * DONE (GenomicAlignments) rm -vf /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library/R.css \ /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments/COPYING \ /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments/LICENSE.txt if test -f debian/overrides; then \ install -d /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/share/lintian/overrides ; \ install -m 0644 debian/overrides \ /«PKGBUILDDIR»/debian/r-bioc-genomicalignments/usr/share/lintian/overrides/r-bioc-genomicalignments; \ fi Adding cdbs dependencies to debian/r-bioc-genomicalignments.substvars dh_installdirs -pr-bioc-genomicalignments dh_installdocs -pr-bioc-genomicalignments ./NEWS dh_installexamples -pr-bioc-genomicalignments dh_installman -pr-bioc-genomicalignments dh_installinfo -pr-bioc-genomicalignments dh_installmenu -pr-bioc-genomicalignments dh_installcron -pr-bioc-genomicalignments dh_installinit -pr-bioc-genomicalignments dh_installdebconf -pr-bioc-genomicalignments dh_installemacsen -pr-bioc-genomicalignments dh_installcatalogs -pr-bioc-genomicalignments dh_installpam -pr-bioc-genomicalignments dh_installlogrotate -pr-bioc-genomicalignments dh_installlogcheck -pr-bioc-genomicalignments dh_installchangelogs -pr-bioc-genomicalignments dh_installudev -pr-bioc-genomicalignments dh_lintian -pr-bioc-genomicalignments dh_bugfiles -pr-bioc-genomicalignments dh_install -pr-bioc-genomicalignments dh_link -pr-bioc-genomicalignments dh_installmime -pr-bioc-genomicalignments dh_installgsettings -pr-bioc-genomicalignments dh_strip -pr-bioc-genomicalignments dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_compress -pr-bioc-genomicalignments dh_fixperms -pr-bioc-genomicalignments dh_makeshlibs -pr-bioc-genomicalignments dh_installdeb -pr-bioc-genomicalignments dh_perl -pr-bioc-genomicalignments dh_shlibdeps -pr-bioc-genomicalignments dh_gencontrol -pr-bioc-genomicalignments dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package r-bioc-genomicalignments: unused substitution variable ${R:Depends} dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform amd64: r-bioc-genomicalignments dh_gencontrol debug symbol wrapper: packages to act on: r-bioc-genomicalignments dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/r-bioc-genomicalignments-dbgsym, skipping package r-bioc-genomicalignments # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -pr-bioc-genomicalignments ; fi dh_md5sums -pr-bioc-genomicalignments dh_builddeb -pr-bioc-genomicalignments INFO: pkgstriptranslations version 121 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `r-bioc-genomicalignments' in `../r-bioc-genomicalignments_1.4.1-1cran1ppa0_amd64.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../genomicalignments_1.4.1-1cran1ppa0_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 genomicalignments-1.4.1 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150915-1651 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ genomicalignments_1.4.1-1cran1ppa0_amd64.changes: ───────────────────────────────────────────────── Format: 1.8 Date: Mon, 11 May 2015 21:39:23 +0000 Source: genomicalignments Binary: r-bioc-genomicalignments Architecture: amd64 Version: 1.4.1-1cran1ppa0 Distribution: trusty Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael Rutter Description: r-bioc-genomicalignments - GNU R package "Representation and manipulation of short Changes: genomicalignments (1.4.1-1cran1ppa0) trusty; urgency=medium . * Compilation for Ubuntu 14.04.2 LTS Checksums-Sha1: 876ebf6276170c4ce1732614401ccc2e5156fb35 1279096 r-bioc-genomicalignments_1.4.1-1cran1ppa0_amd64.deb Checksums-Sha256: cf74269b2309a70a6ff6d225150734825e1b3648272be1fa0b13b6f8be13a797 1279096 r-bioc-genomicalignments_1.4.1-1cran1ppa0_amd64.deb Files: 71d4dd999a962f7c97513b605c513e9d 1279096 gnu-r optional r-bioc-genomicalignments_1.4.1-1cran1ppa0_amd64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ r-bioc-genomicalignments_1.4.1-1cran1ppa0_amd64.deb ─────────────────────────────────────────────────── new debian package, version 2.0. size 1279096 bytes: control archive=2159 bytes. 933 bytes, 22 lines control 4620 bytes, 47 lines md5sums Package: r-bioc-genomicalignments Source: genomicalignments Version: 1.4.1-1cran1ppa0 Architecture: amd64 Maintainer: cran2deb4ubuntu Installed-Size: 1841 Depends: r-base-core, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-biocparallel, libc6 (>= 2.4) Section: gnu-r Priority: optional Description: GNU R package "Representation and manipulation of short genomic alignments" . Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. . Author: Herv\'e Pag\`es, Valerie Obenchain, Martin Morgan . 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└──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 6204 Build-Time: 28 Distribution: trusty Host Architecture: amd64 Install-Time: 34 Job: genomicalignments_1.4.1-1cran1ppa0.dsc Machine Architecture: amd64 Package: genomicalignments Package-Time: 62 Source-Version: 1.4.1-1cran1ppa0 Space: 6204 Status: successful Version: 1.4.1-1cran1ppa0 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150915-1651 Build needed 00:01:02, 6204k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-7904694'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-7904694/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-7904694'] Unmounting chroot for build PACKAGEBUILD-7904694... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-7904694'] Removing build PACKAGEBUILD-7904694