RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-56 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... 11 Sep 10:59:29 ntpdate[1646]: adjust time server 10.211.37.1 offset -0.019218 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-7896912', '/home/buildd/filecache-default/bcd5dc063ce51e1147d70d5a7a54c6f9cc3d3ea4'] Unpacking chroot for build PACKAGEBUILD-7896912 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-7896912'] Mounting chroot for build PACKAGEBUILD-7896912 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-7896912', '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-7896912 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-7896912', 'amd64'] Updating debian chroot for build PACKAGEBUILD-7896912 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://ftpmaster.internal trusty-security Release.gpg [933 B] Get:4 http://ppa.launchpad.net trusty Release.gpg [316 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://ppa.launchpad.net trusty/main amd64 Packages [49.4 kB] Ign http://ppa.launchpad.net trusty Release Get:11 http://ppa.launchpad.net trusty/main Translation-en [45.1 kB] Get:12 http://ftpmaster.internal trusty-updates Release [63.5 kB] Get:13 http://ppa.launchpad.net trusty/main amd64 Packages [8010 B] Get:14 http://ppa.launchpad.net trusty/main Translation-en [7147 B] Get:15 http://ftpmaster.internal trusty/main amd64 Packages [1350 kB] Get:16 http://ftpmaster.internal trusty/restricted amd64 Packages [13.0 kB] Get:17 http://ftpmaster.internal trusty/universe amd64 Packages [5859 kB] 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 5s (2546 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 2s (23.1 MB/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-7896912', 'amd64', 'trusty', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=trusty', '--purge=never', '--nolog', 'berkeley-express_1.5.1-1biolinux1.dsc'] Initiating build PACKAGEBUILD-7896912 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 lgw01-56.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ berkeley-express 1.5.1-1biolinux1 (amd64) 11 Sep 2015 11:00 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: berkeley-express Version: 1.5.1-1biolinux1 Source Version: 1.5.1-1biolinux1 Distribution: trusty Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/berkeley-express-WPTCdi/berkeley-express-1.5.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/berkeley-express-WPTCdi' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-7896912/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── berkeley-express_1.5.1-1biolinux1.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-qJNpEb/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), debhelper (>= 9), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler 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), debhelper (>= 9), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler dpkg-deb: building package `sbuild-build-depends-berkeley-express-dummy' in `/«BUILDDIR»/resolver-Tk3eH2/apt_archive/sbuild-build-depends-berkeley-express-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 berkeley-express build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cmake cmake-data debhelper dh-apparmor file gettext gettext-base groff-base intltool-debian libarchive13 libasprintf0c2 libbamtools-dev libbamtools2.4.0 libboost-atomic1.54-dev libboost-atomic1.54.0 libboost-chrono1.54-dev libboost-chrono1.54.0 libboost-date-time-dev libboost-date-time1.54-dev libboost-date-time1.54.0 libboost-filesystem-dev libboost-filesystem1.54-dev libboost-filesystem1.54.0 libboost-program-options-dev libboost-program-options1.54-dev libboost-program-options1.54.0 libboost-serialization1.54-dev libboost-serialization1.54.0 libboost-system-dev libboost-system1.54-dev libboost-system1.54.0 libboost-thread-dev libboost-thread1.54-dev libboost-thread1.54.0 libboost-tools-dev libboost1.54-dev libboost1.54-tools-dev libcroco3 libcurl3 libexpat1 libglib2.0-0 libgoogle-perftools-dev libgoogle-perftools4 liblzo2-2 libmagic1 libnettle4 libpipeline1 libprotobuf-dev libprotobuf-lite8 libprotobuf8 libprotoc8 libtcmalloc-minimal4 libunistring0 libunwind8 libunwind8-dev libxml2 man-db po-debconf protobuf-compiler zlib1g-dev Suggested packages: wamerican wordlist whois vacation codeblocks eclipse dh-make apparmor-easyprof gettext-doc groff lrzip libboost1.54-doc libboost-context1.54-dev libboost-coroutine.54-dev libboost-exception1.54-dev libboost-graph1.54-dev libboost-graph-parallel1.54-dev libboost-iostreams1.54-dev libboost-locale1.54-dev libboost-log.54-dev libboost-math1.54-dev libboost-mpi1.54-dev libboost-mpi-python1.54-dev libboost-python1.54-dev libboost-random1.54-dev libboost-regex1.54-dev libboost-signals1.54-dev libboost-test1.54-dev libboost-timer1.54-dev libboost-wave1.54-dev libmpfrc++-dev libntl-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cmake cmake-data debhelper dh-apparmor file gettext gettext-base groff-base intltool-debian libarchive13 libasprintf0c2 libbamtools-dev libbamtools2.4.0 libboost-atomic1.54-dev libboost-atomic1.54.0 libboost-chrono1.54-dev libboost-chrono1.54.0 libboost-date-time-dev libboost-date-time1.54-dev libboost-date-time1.54.0 libboost-filesystem-dev libboost-filesystem1.54-dev libboost-filesystem1.54.0 libboost-program-options-dev libboost-program-options1.54-dev libboost-program-options1.54.0 libboost-serialization1.54-dev libboost-serialization1.54.0 libboost-system-dev libboost-system1.54-dev libboost-system1.54.0 libboost-thread-dev libboost-thread1.54-dev libboost-thread1.54.0 libboost-tools-dev libboost1.54-dev libboost1.54-tools-dev libcroco3 libcurl3 libexpat1 libglib2.0-0 libgoogle-perftools-dev libgoogle-perftools4 liblzo2-2 libmagic1 libnettle4 libpipeline1 libprotobuf-dev libprotobuf-lite8 libprotobuf8 libprotoc8 libtcmalloc-minimal4 libunistring0 libunwind8 libunwind8-dev libxml2 man-db po-debconf protobuf-compiler sbuild-build-depends-berkeley-express-dummy zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 20.2 MB/20.2 MB of archives. After this operation, 165 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libbamtools2.4.0 libbamtools-dev sbuild-build-depends-berkeley-express-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://ftpmaster.internal/ubuntu/ trusty-security/main libmagic1 amd64 1:5.14-2ubuntu3.3 [185 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-updates/main libasprintf0c2 amd64 0.18.3.1-1ubuntu3 [6712 B] Get:4 http://ftpmaster.internal/ubuntu/ trusty-updates/main libglib2.0-0 amd64 2.40.2-0ubuntu1 [1058 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libpipeline1 amd64 1.3.0-1 [24.0 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty-security/main libxml2 amd64 2.9.1+dfsg1-3ubuntu4.4 [570 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main groff-base amd64 1.22.2-5 [1053 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty-updates/main man-db amd64 2.6.7.1-1ubuntu1 [857 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty-security/main liblzo2-2 amd64 2.06-1.2ubuntu1.1 [46.1 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libnettle4 amd64 2.7.1-1 [121 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty-security/main libarchive13 amd64 3.1.2-7ubuntu2.1 [259 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-atomic1.54.0 amd64 1.54.0-4ubuntu3.1 [8076 B] Get:14 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-system1.54.0 amd64 1.54.0-4ubuntu3.1 [10.1 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-chrono1.54.0 amd64 1.54.0-4ubuntu3.1 [12.5 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-date-time1.54.0 amd64 1.54.0-4ubuntu3.1 [20.8 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-filesystem1.54.0 amd64 1.54.0-4ubuntu3.1 [34.2 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-program-options1.54.0 amd64 1.54.0-4ubuntu3.1 [115 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-serialization1.54.0 amd64 1.54.0-4ubuntu3.1 [126 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-thread1.54.0 amd64 1.54.0-4ubuntu3.1 [26.5 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty-security/main libcurl3 amd64 7.35.0-1ubuntu2.5 [173 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty/main libunwind8 amd64 1.1-2.2ubuntu3 [48.3 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty-security/main file amd64 1:5.14-2ubuntu3.3 [18.9 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext-base amd64 0.18.3.1-1ubuntu3 [48.8 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main cmake-data all 2.8.12.2-0ubuntu3 [676 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main cmake amd64 2.8.12.2-0ubuntu3 [2618 kB] Get:29 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main libbamtools2.4.0 amd64 2.4.0+dfsg-1biolinux1 [163 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty-updates/main gettext amd64 0.18.3.1-1ubuntu3 [829 kB] Get:31 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main libbamtools-dev amd64 2.4.0+dfsg-1biolinux1 [208 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty-updates/main dh-apparmor all 2.8.95~2430-0ubuntu5.3 [12.2 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost1.54-dev amd64 1.54.0-4ubuntu3.1 [5682 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-atomic1.54-dev amd64 1.54.0-4ubuntu3.1 [4914 B] Get:38 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-chrono1.54-dev amd64 1.54.0-4ubuntu3.1 [14.2 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-serialization1.54-dev amd64 1.54.0-4ubuntu3.1 [151 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-date-time1.54-dev amd64 1.54.0-4ubuntu3.1 [25.2 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main libboost-date-time-dev amd64 1.54.0.1ubuntu1 [2826 B] Get:42 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-system1.54-dev amd64 1.54.0-4ubuntu3.1 [8428 B] Get:43 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-filesystem1.54-dev amd64 1.54.0-4ubuntu3.1 [41.7 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main libboost-filesystem-dev amd64 1.54.0.1ubuntu1 [2854 B] Get:45 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-program-options1.54-dev amd64 1.54.0-4ubuntu3.1 [133 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main libboost-program-options-dev amd64 1.54.0.1ubuntu1 [2840 B] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main libboost-system-dev amd64 1.54.0.1ubuntu1 [2956 B] Get:48 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost-thread1.54-dev amd64 1.54.0-4ubuntu3.1 [26.0 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main libboost-thread-dev amd64 1.54.0.1ubuntu1 [2848 B] Get:50 http://ftpmaster.internal/ubuntu/ trusty-updates/main libboost1.54-tools-dev amd64 1.54.0-4ubuntu3.1 [1048 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/universe libboost-tools-dev amd64 1.54.0.1ubuntu1 [2992 B] Get:52 http://ftpmaster.internal/ubuntu/ trusty-updates/main libtcmalloc-minimal4 amd64 2.1-2ubuntu1.1 [103 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgoogle-perftools4 amd64 2.1-2ubuntu1.1 [184 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libunwind8-dev amd64 1.1-2.2ubuntu3 [375 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty-updates/main libgoogle-perftools-dev amd64 2.1-2ubuntu1.1 [407 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libprotobuf-lite8 amd64 2.5.0-9ubuntu1 [52.7 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main libprotobuf8 amd64 2.5.0-9ubuntu1 [296 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main libprotoc8 amd64 2.5.0-9ubuntu1 [235 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main libprotobuf-dev amd64 2.5.0-9ubuntu1 [421 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main protobuf-compiler amd64 2.5.0-9ubuntu1 [19.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.2 MB in 2s (6903 kB/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 libxml2:amd64. 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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 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 cmake_2.8.12.2-0ubuntu3 cmake-data_2.8.12.2-0ubuntu3 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 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 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 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-debian_0.35.0+20060710.1 iproute2_3.12.0-2ubuntu1 klibc-utils_2.0.3-0ubuntu1 kmod_15-0ubuntu6 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libboost-serialization1.54-dev_1.54.0-4ubuntu3.1 libboost-serialization1.54.0_1.54.0-4ubuntu3.1 libboost-system-dev_1.54.0.1ubuntu1 libboost-system1.54-dev_1.54.0-4ubuntu3.1 libboost-system1.54.0_1.54.0-4ubuntu3.1 libboost-thread-dev_1.54.0.1ubuntu1 libboost-thread1.54-dev_1.54.0-4ubuntu3.1 libboost-thread1.54.0_1.54.0-4ubuntu3.1 libboost-tools-dev_1.54.0.1ubuntu1 libboost1.54-dev_1.54.0-4ubuntu3.1 libboost1.54-tools-dev_1.54.0-4ubuntu3.1 libbz2-1.0_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 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 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 libexpat1_2.1.0-4ubuntu1.1 libfakeroot_1.20-3ubuntu2 libffi6_3.1~rc1+r3.0.13-12 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 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 libgoogle-perftools-dev_2.1-2ubuntu1.1 libgoogle-perftools4_2.1-2ubuntu1.1 libgpg-error0_1.12-0.2ubuntu1 libgssapi-krb5-2_1.12+dfsg-2ubuntu5.1 libgssapi3-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libhcrypto4-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimbase1-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libheimntlm0-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libhx509-5-heimdal_1.6~git20131207+dfsg-1ubuntu1.1 libidn11_1.28-1ubuntu2 libisl10_0.12.2-1 libitm1_4.8.4-2ubuntu1~14.04 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 libldap-2.4-2_2.4.31-1+nmu2ubuntu8.1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 liblzo2-2_2.06-1.2ubuntu1.1 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 libncursesw5_5.9+20140118-1ubuntu1 libnettle4_2.7.1-1 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 libpcre3_1:8.31-2ubuntu2.1 libpipeline1_1.3.0-1 libplymouth2_0.8.8-0ubuntu17.1 libpng12-0_1.2.50-1ubuntu2 libprocps3_1:3.3.9-1ubuntu2.2 libprotobuf-dev_2.5.0-9ubuntu1 libprotobuf-lite8_2.5.0-9ubuntu1 libprotobuf8_2.5.0-9ubuntu1 libprotoc8_2.5.0-9ubuntu1 libquadmath0_4.8.4-2ubuntu1~14.04 libreadline6_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 libslang2_2.2.4-15ubuntu1 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 libtcmalloc-minimal4_2.1-2ubuntu1.1 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1ubuntu1 libtsan0_4.8.4-2ubuntu1~14.04 libudev1_204-5ubuntu20.13 libunistring0_0.9.3-5ubuntu3 libunwind8_1.1-2.2ubuntu3 libunwind8-dev_1.1-2.2ubuntu3 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 libxml2_2.9.1+dfsg1-3ubuntu4.4 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 make_3.81-8.2ubuntu3 makedev_2.3.1-93ubuntu1 man-db_2.6.7.1-1ubuntu1 mawk_1.3.3-17ubuntu2 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 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 protobuf-compiler_2.5.0-9ubuntu1 readline-common_6.3-4ubuntu2 sbuild-build-depends-berkeley-express-dummy_0.invalid.0 sbuild-build-depends-core-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 udev_204-5ubuntu20.13 upstart_1.12.1-0ubuntu4.2 util-linux_2.20.1-5.1ubuntu20.6 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-1ubuntu1 zlib1g-dev_1:1.2.8.dfsg-1ubuntu1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Fri Sep 11 10:58:29 2015 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./berkeley-express_1.5.1-1biolinux1.dsc dpkg-source: info: extracting berkeley-express in berkeley-express-1.5.1 dpkg-source: info: unpacking berkeley-express_1.5.1.orig.tar.gz dpkg-source: info: unpacking berkeley-express_1.5.1-1biolinux1.debian.tar.gz dpkg-source: info: applying spelling-fixes dpkg-source: info: applying fix-bamtools-path dpkg-source: info: applying drop-zlib 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 berkeley-express dpkg-buildpackage: source version 1.5.1-1biolinux1 dpkg-buildpackage: source distribution trusty dpkg-source --before-build berkeley-express-1.5.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_clean src/config.h make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_auto_configure -a -O--parallel -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Boost version: 1.54.0 -- Found the following Boost libraries: -- thread -- system -- filesystem -- program_options -- date_time -- Found GPERFTOOLS_TCMALLOC: /usr/lib/libtcmalloc.so -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found PROTOBUF: /usr/lib/x86_64-linux-gnu/libprotobuf.so -- Configuring done -- Generating done -- Build files have been written to: /«PKGBUILDDIR»/obj-x86_64-linux-gnu dh_auto_build -a -O--parallel make[1]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -H/«PKGBUILDDIR» -B/«PKGBUILDDIR»/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 2 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 1 [ 11%] [ 11%] Running C++ protocol buffer compiler on /«PKGBUILDDIR»/src/targets.proto Running C++ protocol buffer compiler on /«PKGBUILDDIR»/src/alignments.proto cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src -I /«PKGBUILDDIR»/src /«PKGBUILDDIR»/src/alignments.proto cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src -I /«PKGBUILDDIR»/src /«PKGBUILDDIR»/src/targets.proto cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/src /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= Scanning dependencies of target express make[3]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 3 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 4 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 5 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 6 [ 17%] [ 23%] [ 29%] [ 35%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /«PKGBUILDDIR»/src/mismatchmodel.cpp Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/biascorrection.cpp.o -c /«PKGBUILDDIR»/src/biascorrection.cpp Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/mapparser.cpp.o -c /«PKGBUILDDIR»/src/mapparser.cpp cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/markovmodel.cpp.o -c /«PKGBUILDDIR»/src/markovmodel.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 7 [ 41%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/threadsafety.cpp.o -c /«PKGBUILDDIR»/src/threadsafety.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 8 [ 47%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/fragments.cpp.o -c /«PKGBUILDDIR»/src/fragments.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 9 [ 52%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /«PKGBUILDDIR»/src/robertsfilter.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 10 [ 58%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/bundles.cpp.o -c /«PKGBUILDDIR»/src/bundles.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 11 [ 64%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /«PKGBUILDDIR»/src/lengthdistribution.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 12 [ 70%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/targets.cpp.o -c /«PKGBUILDDIR»/src/targets.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 13 [ 76%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/main.cpp.o -c /«PKGBUILDDIR»/src/main.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 14 [ 82%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/sequence.cpp.o -c /«PKGBUILDDIR»/src/sequence.cpp /«PKGBUILDDIR»/src/targets.cpp: In member function 'void TargetTable::output_results(std::string, size_t, bool, bool)': /«PKGBUILDDIR»/src/targets.cpp:667:16: warning: variable 'count_var' set but not used [-Wunused-but-set-variable] double count_var = 0; ^ In file included from /«PKGBUILDDIR»/src/main.cpp:42:0: /«PKGBUILDDIR»/src/update_check.h: In function 'bool get_current_version(char*)': /«PKGBUILDDIR»/src/update_check.h:89:28: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 15 [ 88%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/directiondetector.cpp.o -c /«PKGBUILDDIR»/src/directiondetector.cpp /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 16 [ 94%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/alignments.pb.cc.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/alignments.pb.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 17 [100%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -I/usr/include/bamtools -o CMakeFiles/express.dir/targets.pb.cc.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/targets.pb.cc Linking CXX executable express cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -Wall -O3 -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/express.dir/biascorrection.cpp.o CMakeFiles/express.dir/mismatchmodel.cpp.o CMakeFiles/express.dir/mapparser.cpp.o CMakeFiles/express.dir/markovmodel.cpp.o CMakeFiles/express.dir/threadsafety.cpp.o CMakeFiles/express.dir/fragments.cpp.o CMakeFiles/express.dir/robertsfilter.cpp.o CMakeFiles/express.dir/bundles.cpp.o CMakeFiles/express.dir/lengthdistribution.cpp.o CMakeFiles/express.dir/targets.cpp.o CMakeFiles/express.dir/main.cpp.o CMakeFiles/express.dir/sequence.cpp.o CMakeFiles/express.dir/directiondetector.cpp.o CMakeFiles/express.dir/alignments.pb.cc.o CMakeFiles/express.dir/targets.pb.cc.o -o express -rdynamic -Wl,-Bstatic -lboost_thread -lboost_system -lboost_filesystem -lboost_program_options -lboost_date_time -Wl,-Bdynamic -lpthread -lbamtools -lpthread -Wl,-Bstatic -lprotobuf -Wl,-Bdynamic make[3]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 [100%] Built target express make[2]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' dh_auto_test -a -O--parallel fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel dh_installdirs -a -O--parallel dh_auto_install -a -O--parallel make[1]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -H/«PKGBUILDDIR» -B/«PKGBUILDDIR»/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/src /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= make[3]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[3]: Nothing to be done for `src/CMakeFiles/express.dir/build'. make[3]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 [100%] Built target express make[2]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[2]: Nothing to be done for `preinstall'. make[2]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /«PKGBUILDDIR»/debian/tmp/usr/bin/express make[1]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' dh_install -a -O--parallel dh_installdocs -a 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ignored packages: dh_gencontrol debug symbol wrapper: no debian/berkeley-express-dbgsym, skipping package berkeley-express dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel 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 `berkeley-express' in `../berkeley-express_1.5.1-1biolinux1_amd64.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../berkeley-express_1.5.1-1biolinux1_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 berkeley-express-1.5.1 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150911-1100 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ berkeley-express_1.5.1-1biolinux1_amd64.changes: ──────────────────────────────────────────────── Format: 1.8 Date: Thu, 10 Sep 2015 17:22:12 +0100 Source: berkeley-express Binary: berkeley-express berkeley-express-doc Architecture: amd64 Version: 1.5.1-1biolinux1 Distribution: trusty Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Tim Booth Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Changes: berkeley-express (1.5.1-1biolinux1) trusty; urgency=medium . * Backport to Trusty * Backported libbamtools to enable this build Checksums-Sha1: 218df3a82f12f927e5bb207a2f1217547a8ea203 550462 berkeley-express_1.5.1-1biolinux1_amd64.deb Checksums-Sha256: 05ebf0e7a2c53cb381d4a843061aa36523fa9bbfbd17930069d1f948a7ce4bfa 550462 berkeley-express_1.5.1-1biolinux1_amd64.deb Files: 6c6ae21dce9c7271eaf9f17d42bc88ee 550462 science optional berkeley-express_1.5.1-1biolinux1_amd64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ berkeley-express_1.5.1-1biolinux1_amd64.deb ─────────────────────────────────────────── new debian package, version 2.0. size 550462 bytes: control archive=1786 bytes. 2956 bytes, 50 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.1-1biolinux1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1984 Depends: libbamtools2.4.0, libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6) Recommends: med-config (>= 2.1) Section: science Priority: optional Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. drwxr-xr-x root/root 0 2015-09-11 11:00 ./ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/bin/ lrwxrwxrwx root/root 0 2015-09-11 11:00 ./usr/bin/berkeley-express -> ../lib/debian-med/bin/express drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/lib/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 1975304 2015-09-11 11:00 ./usr/lib/debian-med/bin/express drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/share/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/share/doc/berkeley-express/ -rw-r--r-- root/root 987 2015-09-10 16:18 ./usr/share/doc/berkeley-express/README.Debian -rw-r--r-- root/root 1540 2013-12-08 19:09 ./usr/share/doc/berkeley-express/README.gz -rw-r--r-- root/root 270 2015-09-11 10:58 ./usr/share/doc/berkeley-express/changelog.Debian.gz -rw-r--r-- root/root 2668 2015-09-10 16:18 ./usr/share/doc/berkeley-express/copyright drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/share/man/ drwxr-xr-x root/root 0 2015-09-11 11:00 ./usr/share/man/man1/ -rw-r--r-- root/root 1192 2015-09-11 11:00 ./usr/share/man/man1/berkeley-express.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 14988 Build-Time: 33 Distribution: trusty Host Architecture: amd64 Install-Time: 16 Job: berkeley-express_1.5.1-1biolinux1.dsc Machine Architecture: amd64 Package: berkeley-express Package-Time: 49 Source-Version: 1.5.1-1biolinux1 Space: 14988 Status: successful Version: 1.5.1-1biolinux1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150911-1100 Build needed 00:00:49, 14988k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-7896912'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-7896912/chroot-autobuild... 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