RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-38 4.4.0-92-generic #115-Ubuntu SMP Thu Aug 10 09:04:33 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_147 python-lpbuildd_147 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.2 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 22 Aug 23:08:12 ntpdate[1764]: adjust time server 10.211.37.1 offset 0.018359 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-13283256', '/home/buildd/filecache-default/e3a0751dad18cad81698aa46cb02fd9a2acf7c0b'] Unpacking chroot for build PACKAGEBUILD-13283256 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-13283256'] Mounting chroot for build PACKAGEBUILD-13283256 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-13283256', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-13283256 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-13283256', 'amd64'] Updating debian chroot for build PACKAGEBUILD-13283256 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 Packages [1137 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [560 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe amd64 Packages [8237 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4780 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 Packages [135 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [61.3 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe amd64 Packages [411 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [191 kB] Fetched 16.1 MB in 3s (4208 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-7 g++-7 gcc-7 gcc-7-base libasan4 libgcc-7-dev libperl5.26 libstdc++-7-dev perl-modules-5.26 The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcilkrts5 libcomerr2 libcryptsetup4 libcurl3-gnutls libdb5.3 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libip4tc0 libitm1 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblsan0 liblzma5 libmount1 libmpx2 libnpth0 libp11-kit0 libpcre3 libpng16-16 libpsl5 libquadmath0 libroken18-heimdal libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd perl perl-base sensible-utils systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 118 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 170 MB of archives. After this operation, 552 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main amd64 debconf all 1.5.63 [136 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 perl-modules-5.26 all 5.26.0-5 [2762 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main amd64 libperl5.26 amd64 5.26.0-5 [3523 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 perl amd64 5.26.0-5 [205 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 perl-base amd64 5.26.0-5 [1380 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main amd64 libc6-dev amd64 2.24-12ubuntu1 [2278 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main amd64 libc-dev-bin amd64 2.24-12ubuntu1 [68.6 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 linux-libc-dev amd64 4.12.0-12.13 [956 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 gcc-7-base amd64 7.2.0-1ubuntu1 [17.9 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libgcc1 amd64 1:7.2.0-1ubuntu1 [39.4 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main amd64 libc6 amd64 2.24-12ubuntu1 [2590 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main amd64 libdb5.3 amd64 5.3.28-13 [670 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 zlib1g amd64 1:1.2.11.dfsg-0ubuntu2 [56.5 kB] Get:14 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init-system-helpers all 1.49 [37.0 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 base-files amd64 9.6ubuntu101 [59.1 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main amd64 debianutils amd64 4.8.2 [86.1 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main amd64 bash amd64 4.4-5ubuntu1 [625 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main amd64 bsdutils amd64 1:2.30.1-0ubuntu3 [59.7 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main amd64 diffutils amd64 1:3.6-1 [167 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 tar amd64 1.29b-2 [233 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg amd64 1.18.24ubuntu1 [1140 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 e2fslibs amd64 1.43.5-1 [156 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 e2fsprogs amd64 1.43.5-1 [497 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 findutils amd64 4.6.0+git+20170729-2 [291 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 grep amd64 3.1-2 [158 kB] Get:26 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 login amd64 1:4.2-3.2ubuntu4 [305 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main amd64 libuuid1 amd64 2.30.1-0ubuntu3 [14.5 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main amd64 libblkid1 amd64 2.30.1-0ubuntu3 [118 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 libpcre3 amd64 2:8.39-4 [227 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main amd64 libselinux1 amd64 2.6-3build2 [67.7 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main amd64 libmount1 amd64 2.30.1-0ubuntu3 [131 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main amd64 libfdisk1 amd64 2.30.1-0ubuntu3 [157 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main amd64 libsmartcols1 amd64 2.30.1-0ubuntu3 [78.7 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main amd64 util-linux amd64 2.30.1-0ubuntu3 [942 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main amd64 mount amd64 2.30.1-0ubuntu3 [130 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main amd64 libc-bin amd64 2.24-12ubuntu1 [634 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main amd64 liblzma5 amd64 5.2.2-1.3 [90.8 kB] Get:38 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libstdc++6 amd64 7.2.0-1ubuntu1 [405 kB] Get:39 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapt-pkg5.0 amd64 1.5~beta2 [780 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main amd64 libtasn1-6 amd64 4.12-2.1 [35.8 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main amd64 libp11-kit0 amd64 0.23.7-3 [187 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main amd64 libgnutls30 amd64 3.5.8-6ubuntu2 [678 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main amd64 libk5crypto3 amd64 1.15.1-2 [84.9 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main amd64 libgssapi-krb5-2 amd64 1.15.1-2 [120 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5-3 amd64 1.15.1-2 [276 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5support0 amd64 1.15.1-2 [32.2 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main amd64 libcomerr2 amd64 1.43.5-1 [10.7 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main amd64 libidn2-0 amd64 2.0.2-3 [91.3 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1ubuntu1 [155 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main amd64 libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main amd64 libroken18-heimdal amd64 7.4.0.dfsg.1-2 [40.9 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main amd64 libasn1-8-heimdal amd64 7.4.0.dfsg.1-2 [177 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main amd64 libheimbase1-heimdal amd64 7.4.0.dfsg.1-2 [29.2 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main amd64 libhcrypto4-heimdal amd64 7.4.0.dfsg.1-2 [88.1 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main amd64 libwind0-heimdal amd64 7.4.0.dfsg.1-2 [47.8 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main amd64 libhx509-5-heimdal amd64 7.4.0.dfsg.1-2 [107 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main amd64 libsqlite3-0 amd64 3.19.3-3 [493 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5-26-heimdal amd64 7.4.0.dfsg.1-2 [207 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main amd64 libheimntlm0-heimdal amd64 7.4.0.dfsg.1-2 [15.1 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main amd64 libgssapi3-heimdal amd64 7.4.0.dfsg.1-2 [97.3 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu1 [14.7 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu1 [49.0 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main amd64 libpsl5 amd64 0.18.0-2 [40.6 kB] Get:64 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libcurl3-gnutls amd64 7.55.0-1ubuntu1 [193 kB] Get:65 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt-transport-https amd64 1.5~beta2 [34.7 kB] Get:66 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt amd64 1.5~beta2 [1118 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main amd64 libip4tc0 amd64 1.6.1-2ubuntu1 [19.6 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main amd64 libapparmor1 amd64 2.11.0-2ubuntu16 [28.9 kB] Get:69 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libaudit-common all 1:2.7.7-1ubuntu2 [3998 B] Get:70 http://ftpmaster.internal/ubuntu artful/main amd64 libcap-ng0 amd64 0.7.7-3build1 [10.9 kB] Get:71 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libaudit1 amd64 1:2.7.7-1ubuntu2 [38.1 kB] Get:72 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libudev1 amd64 234-2ubuntu8 [52.8 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main amd64 libdevmapper1.02.1 amd64 2:1.02.137-2ubuntu3 [135 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main amd64 libgpg-error0 amd64 1.27-3 [36.4 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main amd64 libgcrypt20 amd64 1.7.8-2 [400 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main amd64 libcryptsetup4 amd64 2:1.7.2-0ubuntu4 [75.4 kB] Get:77 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libkmod2 amd64 24-1ubuntu2 [40.1 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd amd64 234-2ubuntu8 [2772 kB] Get:79 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libsystemd0 amd64 234-2ubuntu8 [209 kB] Get:80 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init amd64 1.49 [6040 B] Get:81 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd-sysv amd64 234-2ubuntu8 [11.9 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage-common all 2.6-2build2 [6682 B] Get:83 http://ftpmaster.internal/ubuntu artful/main amd64 libsemanage1 amd64 2.6-2build2 [82.7 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main amd64 libss2 amd64 1.43.5-1 [11.0 kB] Get:85 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 passwd amd64 1:4.2-3.2ubuntu4 [786 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main amd64 sensible-utils all 0.0.10 [14.6 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main amd64 dmsetup amd64 2:1.02.137-2ubuntu3 [71.9 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main amd64 libassuan0 amd64 2.4.3-3 [34.8 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main amd64 libnpth0 amd64 1.5-2 [7622 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http://ftpmaster.internal/ubuntu artful/main amd64 cpp amd64 4:7.1.0-1ubuntu3 [27.6 kB] Get:101 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libquadmath0 amd64 7.2.0-1ubuntu1 [132 kB] Get:102 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libitm1 amd64 7.2.0-1ubuntu1 [27.6 kB] Get:103 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libmpx2 amd64 7.2.0-1ubuntu1 [11.7 kB] Get:104 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 liblsan0 amd64 7.2.0-1ubuntu1 [127 kB] Get:105 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libtsan0 amd64 7.2.0-1ubuntu1 [276 kB] Get:106 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libubsan0 amd64 7.2.0-1ubuntu1 [119 kB] Get:107 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libcilkrts5 amd64 7.2.0-1ubuntu1 [42.5 kB] Get:108 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libgomp1 amd64 7.2.0-1ubuntu1 [76.5 kB] Get:109 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libatomic1 amd64 7.2.0-1ubuntu1 [8954 B] Get:110 http://ftpmaster.internal/ubuntu artful/main amd64 libasan3 amd64 6.4.0-4ubuntu1 [315 kB] Get:111 http://ftpmaster.internal/ubuntu artful/universe amd64 g++-6 amd64 6.4.0-4ubuntu1 [7404 kB] Get:112 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++-6-dev amd64 6.4.0-4ubuntu1 [1429 kB] Get:113 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6 amd64 6.4.0-4ubuntu1 [7243 kB] Get:114 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc-6-dev amd64 6.4.0-4ubuntu1 [2305 kB] Get:115 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libcc1-0 amd64 7.2.0-1ubuntu1 [38.6 kB] Get:116 http://ftpmaster.internal/ubuntu artful/main amd64 cpp-6 amd64 6.4.0-4ubuntu1 [6588 kB] Get:117 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6-base amd64 6.4.0-4ubuntu1 [16.6 kB] Get:118 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:119 http://ftpmaster.internal/ubuntu artful/main amd64 libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:120 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libasan4 amd64 7.2.0-1ubuntu1 [353 kB] Get:121 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libgcc-7-dev amd64 7.2.0-1ubuntu1 [2366 kB] Get:122 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 gcc-7 amd64 7.2.0-1ubuntu1 [32.7 MB] Get:123 http://ftpmaster.internal/ubuntu artful/main amd64 gcc amd64 4:7.1.0-1ubuntu3 [5270 B] Get:124 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libstdc++-7-dev amd64 7.2.0-1ubuntu1 [1451 kB] Get:125 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 g++-7 amd64 7.2.0-1ubuntu1 [35.9 MB] Get:126 http://ftpmaster.internal/ubuntu artful/main amd64 g++ amd64 4:7.1.0-1ubuntu3 [1480 B] Get:127 http://ftpmaster.internal/ubuntu artful/main amd64 libusb-0.1-4 amd64 2:0.1.12-31 [17.1 kB] debconf: delaying package configuration, since apt-utils is not installed 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Installing new version of config file /etc/systemd/resolved.conf ... Created symlink /etc/systemd/system/dbus-org.freedesktop.resolve1.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-resolved.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/dbus-org.freedesktop.network1.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-networkd.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/sockets.target.wants/systemd-networkd.socket -> /lib/systemd/system/systemd-networkd.socket. Created symlink /etc/systemd/system/network-online.target.wants/systemd-networkd-wait-online.service -> /lib/systemd/system/systemd-networkd-wait-online.service. addgroup: The group `systemd-journal' already exists as a system group. Exiting. 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Unpacking libdpkg-perl (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Selecting previously unselected package libasan4:amd64. Preparing to unpack .../33-libasan4_7.2.0-1ubuntu1_amd64.deb ... Unpacking libasan4:amd64 (7.2.0-1ubuntu1) ... Selecting previously unselected package libgcc-7-dev:amd64. Preparing to unpack .../34-libgcc-7-dev_7.2.0-1ubuntu1_amd64.deb ... Unpacking libgcc-7-dev:amd64 (7.2.0-1ubuntu1) ... Selecting previously unselected package gcc-7. Preparing to unpack .../35-gcc-7_7.2.0-1ubuntu1_amd64.deb ... Unpacking gcc-7 (7.2.0-1ubuntu1) ... Preparing to unpack .../36-gcc_4%3a7.1.0-1ubuntu3_amd64.deb ... Removing old gcc doc directory. Unpacking gcc (4:7.1.0-1ubuntu3) over (4:6.3.0-2ubuntu1) ... Selecting previously unselected package libstdc++-7-dev:amd64. Preparing to unpack .../37-libstdc++-7-dev_7.2.0-1ubuntu1_amd64.deb ... Unpacking libstdc++-7-dev:amd64 (7.2.0-1ubuntu1) ... Selecting previously unselected package g++-7. Preparing to unpack .../38-g++-7_7.2.0-1ubuntu1_amd64.deb ... Unpacking g++-7 (7.2.0-1ubuntu1) ... Preparing to unpack .../39-g++_4%3a7.1.0-1ubuntu3_amd64.deb ... Unpacking g++ (4:7.1.0-1ubuntu3) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../40-libusb-0.1-4_2%3a0.1.12-31_amd64.deb ... Unpacking libusb-0.1-4:amd64 (2:0.1.12-31) over (2:0.1.12-30) ... Setting up libquadmath0:amd64 (7.2.0-1ubuntu1) ... Setting up libnpth0:amd64 (1.5-2) ... Setting up libgomp1:amd64 (7.2.0-1ubuntu1) ... Setting up libatomic1:amd64 (7.2.0-1ubuntu1) ... Setting up libcc1-0:amd64 (7.2.0-1ubuntu1) ... Setting up libidn2-0:amd64 (2.0.2-3) ... Setting up libssl1.0.0:amd64 (1.0.2g-1ubuntu13) ... Setting up libasan4:amd64 (7.2.0-1ubuntu1) ... Setting up libpng16-16:amd64 (1.6.31-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libcilkrts5:amd64 (7.2.0-1ubuntu1) ... Setting up libpsl5:amd64 (0.18.0-2) ... Setting up multiarch-support (2.24-12ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Aug 22 23:09:12 UTC 2017. Universal Time is now: Tue Aug 22 23:09:12 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu8) ... Setting up libubsan0:amd64 (7.2.0-1ubuntu1) ... Setting up libtsan0:amd64 (7.2.0-1ubuntu1) ... Setting up gcc-6-base:amd64 (6.4.0-4ubuntu1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up linux-libc-dev:amd64 (4.12.0-12.13) ... Setting up advancecomp (2.0-1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up libroken18-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up perl-modules-5.26 (5.26.0-5) ... Setting up libkrb5support0:amd64 (1.15.1-2) ... Setting up cpp-7 (7.2.0-1ubuntu1) ... Setting up liblsan0:amd64 (7.2.0-1ubuntu1) ... Setting up libmpx2:amd64 (7.2.0-1ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libperl5.26:amd64 (5.26.0-5) ... Setting up xz-utils (5.2.2-1.3) ... Setting up libheimbase1-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:amd64 (3.19.3-3) ... Setting up dmsetup (2:1.02.137-2ubuntu3) ... Setting up binutils (2.29-5ubuntu1) ... Setting up cpp-6 (6.4.0-4ubuntu1) ... Setting up libc-dev-bin (2.24-12ubuntu1) ... Setting up ca-certificates (20170717) ... Updating certificates in /etc/ssl/certs... 7 added, 32 removed; done. Setting up libc6-dev:amd64 (2.24-12ubuntu1) ... Setting up libassuan0:amd64 (2.4.3-3) ... Setting up libusb-0.1-4:amd64 (2:0.1.12-31) ... Setting up libitm1:amd64 (7.2.0-1ubuntu1) ... Setting up cpp (4:7.1.0-1ubuntu3) ... Setting up libk5crypto3:amd64 (1.15.1-2) ... Setting up libasan3:amd64 (6.4.0-4ubuntu1) ... Setting up libgcc-6-dev:amd64 (6.4.0-4ubuntu1) ... Setting up libstdc++-6-dev:amd64 (6.4.0-4ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up init (1.49) ... Setting up libasn1-8-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up libhcrypto4-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up libhx509-5-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up libgcc-7-dev:amd64 (7.2.0-1ubuntu1) ... Setting up gcc-6 (6.4.0-4ubuntu1) ... Setting up g++-6 (6.4.0-4ubuntu1) ... Setting up libstdc++-7-dev:amd64 (7.2.0-1ubuntu1) ... Setting up perl (5.26.0-5) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up libkrb5-3:amd64 (1.15.1-2) ... Setting up libkrb5-26-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up libheimntlm0-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up gcc-7 (7.2.0-1ubuntu1) ... Setting up g++-7 (7.2.0-1ubuntu1) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up gcc (4:7.1.0-1ubuntu3) ... Setting up libgssapi-krb5-2:amd64 (1.15.1-2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up g++ (4:7.1.0-1ubuntu3) ... Setting up libgssapi3-heimdal:amd64 (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.55.0-1ubuntu1) ... Setting up apt-transport-https (1.5~beta2) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for ca-certificates (20170717) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-13283256', 'amd64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=artful-proposed', '--purge=never', '--nolog', '-A', 'roary_3.9.1+dfsg-1.dsc'] Initiating build PACKAGEBUILD-13283256 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-92-generic #115-Ubuntu SMP Thu Aug 10 09:04:33 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-38.buildd +==============================================================================+ | roary 3.9.1+dfsg-1 (amd64) 22 Aug 2017 23:09 | +==============================================================================+ Package: roary Version: 3.9.1+dfsg-1 Source Version: 3.9.1+dfsg-1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/roary-jkJnnr/roary-3.9.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/roary-jkJnnr' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13283256/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- roary_3.9.1+dfsg-1.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 '/<>/resolver-dvrwM1/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-dvrwM1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-dvrwM1/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-dvrwM1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-dvrwM1/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-dvrwM1/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (236 kB/s) 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 packages were automatically installed and are no longer required: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'sudo apt autoremove' to remove them. 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-dvrwM1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15383 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl, libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl Filtered Build-Depends: debhelper (>= 10), dh-dist-zilla, libdist-zilla-plugin-podweaver-perl, bioperl, libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, mafft, fasttree, perl dpkg-deb: building package 'sbuild-build-depends-roary-dummy' in '/<>/resolver-zroGYh/apt_archive/sbuild-build-depends-roary-dummy.deb'. Ign:1 copy:/<>/resolver-zroGYh/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zroGYh/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-zroGYh/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zroGYh/apt_archive ./ Sources [433 B] Get:5 copy:/<>/resolver-zroGYh/apt_archive ./ Packages [754 B] Fetched 3306 B in 0s (306 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install roary build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bedtools bioperl bsdmainutils cd-hit debhelper dh-autoreconf dh-dist-zilla dh-strip-nondeterminism fasttree file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libaliased-perl libapp-cmd-perl libarchive-zip-perl libarray-utils-perl libautobox-perl libb-hooks-endofscope-perl libbio-perl-perl libblas-common libblas3 libbsd0 libcairo2 libcapture-tiny-perl libcarp-clan-perl libclass-c3-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-singleton-perl libclone-perl libconfig-ini-perl libconfig-mvp-perl libconfig-mvp-reader-ini-perl libcpan-uploader-perl libcpanel-json-xs-perl libcroco3 libcurl3 libdata-optlist-perl libdata-section-perl libdata-stag-perl libdatetime-locale-perl libdatetime-perl libdatetime-timezone-perl libdatrie1 libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdist-zilla-perl libdist-zilla-plugin-podweaver-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfile-copy-recursive-perl libfile-find-rule-perl libfile-grep-perl libfile-homedir-perl libfile-listing-perl libfile-pushd-perl libfile-sharedir-install-perl libfile-sharedir-perl libfile-slurp-tiny-perl libfile-slurper-perl libfile-stripnondeterminism-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libgetopt-long-descriptive-perl libgfortran4 libglib2.0-0 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b libhash-merge-simple-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libimport-into-perl libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libio-tiecombine-perl libjbig0 libjpeg-turbo8 libjpeg8 libjson-maybexs-perl libjson-perl liblapack3 liblist-moreutils-perl liblog-dispatch-array-perl liblog-dispatch-perl liblog-dispatchouli-perl liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmixin-linewise-perl libmodule-implementation-perl libmodule-path-perl libmodule-pluggable-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-autobox-perl libmoose-perl libmoosex-lazyrequire-perl libmoosex-oneargnew-perl libmoosex-role-parameterized-perl libmoosex-setonce-perl libmoosex-types-perl libmoosex-types-perl-perl libmro-compat-perl libnamespace-autoclean-perl libnamespace-clean-perl libnet-http-perl libnet-ssleay-perl libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparams-validationcompiler-perl libparse-yapp-perl libpath-tiny-perl libperl-prereqscanner-perl libperl-version-perl libperlio-utf8-strict-perl libpipeline1 libpixman-1-0 libpod-elemental-perl libpod-elemental-perlmunger-perl libpod-eventual-perl libpod-weaver-perl libppi-perl libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librole-hasmessage-perl librole-identifiable-perl librole-tiny-perl libscalar-list-utils-perl libscope-guard-perl libsensors4 libsigsegv2 libsm6 libsoftware-license-perl libspecio-perl libspiffy-perl libstrictures-perl libstring-errf-perl libstring-flogger-perl libstring-formatter-perl libstring-rewriteprefix-perl libstring-truncate-perl libsub-exporter-formethods-perl libsub-exporter-globexporter-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsub-uplevel-perl libsyntax-keyword-junction-perl libsyntax-perl libtask-weaken-perl libtcl8.6 libterm-encoding-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-fatal-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtext-template-perl libthai-data libthai0 libthrowable-perl libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtool libtry-tiny-perl liburi-perl libvariable-magic-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxml2 libxrender1 libxss1 libxt6 libyaml-tiny-perl m4 mafft man-db mcl mime-support ncbi-blast+ ncbi-data netbase parallel perl-openssl-defaults po-debconf prank python python-minimal python2.7 python2.7-minimal r-base-core sysstat ucf unzip x11-common xdg-utils zip Suggested packages: autoconf-archive gnu-standards autoconf-doc filo wamerican | wordlist whois vacation dh-make pristine-tar gettext-doc libasprintf-dev libgettextpo-dev groff libxml-sax-expatxs-perl libdata-dump-perl libdb-file-lock-perl libfile-mimeinfo-perl libfile-readbackwards-perl libfreezethaw-perl libmldbm-perl libdbd-csv-perl liblog-dispatch-filerotate-perl librrds-perl libxml-dom-perl libcrypt-ssleay-perl libscalar-number-perl lm-sensors libbareword-filehandles-perl libindirect-perl libmultidimensional-perl tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libauthen-ntlm-perl m4-doc less www-browser mcl-doc libmail-box-perl python-doc python-tk python2.7-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html isag gvfs-bin Recommended packages: bioperl-run perl-doc libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl libxml-simple-perl libyaml-perl libace-perl libxml-twig-perl libset-scalar-perl devscripts curl | wget | lynx-cur libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-sax-perl libxml-sax-writer-perl libxml-libxml-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl bash-completion libarchive-tar-wrapper-perl libterm-readline-gnu-perl libdevel-lexalias-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libjson-xs-perl libmail-sendmail-perl libmailtools-perl libmime-lite-perl libipc-shareable-perl libclass-xsaccessor-perl libdevel-partialdump-perl libunicode-utf8-perl libref-util-perl libtext-csv-xs-perl libltdl-dev libhtml-form-perl libhttp-daemon-perl xml-core blast2 lynx ruby r-recommended r-base-dev r-doc-html cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bedtools bioperl bsdmainutils cd-hit debhelper dh-autoreconf dh-dist-zilla dh-strip-nondeterminism fasttree file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libaliased-perl libapp-cmd-perl libarchive-zip-perl libarray-utils-perl libautobox-perl libb-hooks-endofscope-perl libbio-perl-perl libblas-common libblas3 libbsd0 libcairo2 libcapture-tiny-perl libcarp-clan-perl libclass-c3-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-singleton-perl libclone-perl libconfig-ini-perl libconfig-mvp-perl libconfig-mvp-reader-ini-perl libcpan-uploader-perl libcpanel-json-xs-perl libcroco3 libcurl3 libdata-optlist-perl libdata-section-perl libdata-stag-perl libdatetime-locale-perl libdatetime-perl libdatetime-timezone-perl libdatrie1 libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdist-zilla-perl libdist-zilla-plugin-podweaver-perl libencode-locale-perl libenv-path-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfile-copy-recursive-perl libfile-find-rule-perl libfile-grep-perl libfile-homedir-perl libfile-listing-perl libfile-pushd-perl libfile-sharedir-install-perl libfile-sharedir-perl libfile-slurp-tiny-perl libfile-slurper-perl libfile-stripnondeterminism-perl libfile-which-perl libfindbin-libs-perl libfontconfig1 libfreetype6 libgetopt-long-descriptive-perl libgfortran4 libglib2.0-0 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b libhash-merge-simple-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libimport-into-perl libio-all-perl libio-html-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libio-tiecombine-perl libjbig0 libjpeg-turbo8 libjpeg8 libjson-maybexs-perl libjson-perl liblapack3 liblist-moreutils-perl liblog-dispatch-array-perl liblog-dispatch-perl liblog-dispatchouli-perl liblog-log4perl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmixin-linewise-perl libmodule-implementation-perl libmodule-path-perl libmodule-pluggable-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-autobox-perl libmoose-perl libmoosex-lazyrequire-perl libmoosex-oneargnew-perl libmoosex-role-parameterized-perl libmoosex-setonce-perl libmoosex-types-perl libmoosex-types-perl-perl libmro-compat-perl libnamespace-autoclean-perl libnamespace-clean-perl libnet-http-perl libnet-ssleay-perl libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparams-validationcompiler-perl libparse-yapp-perl libpath-tiny-perl libperl-prereqscanner-perl libperl-version-perl libperlio-utf8-strict-perl libpipeline1 libpixman-1-0 libpod-elemental-perl libpod-elemental-perlmunger-perl libpod-eventual-perl libpod-weaver-perl libppi-perl libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librole-hasmessage-perl librole-identifiable-perl librole-tiny-perl libscalar-list-utils-perl libscope-guard-perl libsensors4 libsigsegv2 libsm6 libsoftware-license-perl libspecio-perl libspiffy-perl libstrictures-perl libstring-errf-perl libstring-flogger-perl libstring-formatter-perl libstring-rewriteprefix-perl libstring-truncate-perl libsub-exporter-formethods-perl libsub-exporter-globexporter-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsub-uplevel-perl libsyntax-keyword-junction-perl libsyntax-perl libtask-weaken-perl libtcl8.6 libterm-encoding-perl libterm-readkey-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-fatal-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtext-template-perl libthai-data libthai0 libthrowable-perl libtie-ixhash-perl libtiff5 libtimedate-perl libtk8.6 libtool libtry-tiny-perl liburi-perl libvariable-magic-perl libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml-parser-perl libxml-writer-perl libxml2 libxrender1 libxss1 libxt6 libyaml-tiny-perl m4 mafft man-db mcl mime-support ncbi-blast+ ncbi-data netbase parallel perl-openssl-defaults po-debconf prank python python-minimal python2.7 python2.7-minimal r-base-core sbuild-build-depends-roary-dummy sysstat ucf unzip x11-common xdg-utils zip 0 upgraded, 270 newly installed, 1 to remove and 0 not upgraded. Need to get 84.0 MB of archives. After this operation, 297 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zroGYh/apt_archive ./ sbuild-build-depends-roary-dummy 0.invalid.0 [1004 B] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:3 http://ftpmaster.internal/ubuntu artful/main amd64 libbsd0 amd64 0.8.6-1 [41.6 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 libxdmcp6 amd64 1:1.1.2-3 [10.7 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main amd64 libx11-data all 2:1.6.4-3 [114 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main amd64 libx11-6 amd64 2:1.6.4-3 [572 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main amd64 groff-base amd64 1.22.3-9 [1144 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main amd64 bsdmainutils amd64 9.0.12+nmu1ubuntu1 [179 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main amd64 libpipeline1 amd64 1.4.2-1 [25.2 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main amd64 man-db amd64 2.7.6.1-2 [895 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main amd64 ucf all 3.0036 [52.9 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 fontconfig-config all 2.11.94-0ubuntu2 [49.9 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main amd64 libexpat1 amd64 2.2.3-1 [72.3 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main amd64 libfreetype6 amd64 2.8-0.2ubuntu1 [333 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main amd64 libfontconfig1 amd64 2.11.94-0ubuntu2 [131 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main amd64 fontconfig amd64 2.11.94-0ubuntu2 [177 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 libjpeg-turbo8 amd64 1.5.1-0ubuntu1 [113 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main amd64 x11-common all 1:7.7+19ubuntu1 [22.1 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 libice6 amd64 2:1.0.9-2 [40.2 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 libxft2 amd64 2.3.2-1 [36.1 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main amd64 libxss1 amd64 1:1.2.2-1 [8582 B] Get:27 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libpython2.7-minimal amd64 2.7.13-4 [342 kB] Get:28 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 python2.7-minimal amd64 2.7.13-4 [1318 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 python-minimal amd64 2.7.13-2 [28.2 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main amd64 mime-support all 3.60ubuntu1 [30.1 kB] Get:31 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libpython2.7-stdlib amd64 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http://ftpmaster.internal/ubuntu artful/main amd64 libicu57 amd64 57.1-6 [7690 kB] Get:43 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libxml2 amd64 2.9.4+dfsg1-3.1 [670 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main amd64 libsigsegv2 amd64 2.11-1 [13.2 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main amd64 autoconf all 2.69-11 [322 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main amd64 autotools-dev all 20161112.1 [39.5 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main amd64 automake all 1:1.15-6ubuntu1 [509 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main amd64 autopoint all 0.19.8.1-2ubuntu2 [411 kB] Get:50 http://ftpmaster.internal/ubuntu artful/universe amd64 bedtools amd64 2.26.0+dfsg-3 [576 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main amd64 libio-string-perl all 1.08-3 [11.1 kB] Get:52 http://ftpmaster.internal/ubuntu artful/universe amd64 libdata-stag-perl all 0.14-1ubuntu2 [366 kB] Get:53 http://ftpmaster.internal/ubuntu artful/universe amd64 libbio-perl-perl all 1.7.1-2 [4572 kB] Get:54 http://ftpmaster.internal/ubuntu artful/universe amd64 bioperl all 1.7.1-2 [387 kB] Get:55 http://ftpmaster.internal/ubuntu artful/universe amd64 cd-hit amd64 4.6.8-1 [516 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main amd64 libtool all 2.4.6-2 [194 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main amd64 dh-autoreconf all 14 [15.5 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-stripnondeterminism-perl all 0.038-1 [13.3 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main amd64 dh-strip-nondeterminism all 0.038-1 [5026 B] Get:62 http://ftpmaster.internal/ubuntu artful/main amd64 libcroco3 amd64 0.6.12-1 [81.3 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main amd64 gettext amd64 0.19.8.1-2ubuntu2 [1092 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main amd64 po-debconf all 1.0.20 [232 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main amd64 debhelper all 10.7.2ubuntu2 [877 kB] Get:67 http://ftpmaster.internal/ubuntu artful/universe amd64 libcapture-tiny-perl all 0.46-1 [20.3 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main amd64 libparams-util-perl amd64 1.07-3build3 [19.6 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main amd64 libsub-install-perl all 0.928-1 [10.5 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main amd64 libdata-optlist-perl all 0.110-1 [9956 B] Get:71 http://ftpmaster.internal/ubuntu artful/main amd64 libparams-classify-perl amd64 0.013-8build1 [21.1 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main amd64 libmodule-runtime-perl all 0.014-2 [15.6 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main amd64 libtry-tiny-perl all 0.28-1 [20.1 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main amd64 libmodule-implementation-perl all 0.09-1 [12.2 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main amd64 libpackage-stash-perl all 0.37-1 [18.3 kB] Get:76 http://ftpmaster.internal/ubuntu artful/universe amd64 libclass-load-perl all 0.24-1 [13.3 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main amd64 libio-stringy-perl all 2.111-2 [60.6 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main amd64 libparams-validate-perl amd64 1.29-1 [52.3 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main amd64 libsub-exporter-perl all 0.986-1 [50.6 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main amd64 libgetopt-long-descriptive-perl all 0.100-1 [24.1 kB] Get:81 http://ftpmaster.internal/ubuntu artful/universe amd64 libio-tiecombine-perl all 1.005-1 [12.5 kB] Get:82 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[5838 B] Get:128 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-which-perl all 1.21-1 [11.8 kB] Get:129 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-homedir-perl all 1.00-1 [46.0 kB] Get:130 http://ftpmaster.internal/ubuntu artful/main amd64 perl-openssl-defaults amd64 3 [6818 B] Get:131 http://ftpmaster.internal/ubuntu artful/main amd64 libnet-ssleay-perl amd64 1.80-1build1 [265 kB] Get:132 http://ftpmaster.internal/ubuntu artful/main amd64 libio-socket-ssl-perl all 2.050-1 [168 kB] Get:133 http://ftpmaster.internal/ubuntu artful/main amd64 liburi-perl all 1.72-1 [76.6 kB] Get:134 http://ftpmaster.internal/ubuntu artful/main amd64 libnet-http-perl all 6.16-1 [22.6 kB] Get:135 http://ftpmaster.internal/ubuntu artful/main amd64 libencode-locale-perl all 1.05-1 [12.3 kB] Get:136 http://ftpmaster.internal/ubuntu artful/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB] Get:137 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-listing-perl all 6.04-1 [9774 B] Get:138 http://ftpmaster.internal/ubuntu artful/main amd64 libhtml-tagset-perl all 3.20-3 [12.1 kB] Get:139 http://ftpmaster.internal/ubuntu artful/main amd64 libhtml-parser-perl amd64 3.72-3build1 [85.9 kB] Get:140 http://ftpmaster.internal/ubuntu artful/main amd64 libhtml-tree-perl all 5.03-2 [197 kB] Get:141 http://ftpmaster.internal/ubuntu artful/main amd64 libio-html-perl all 1.001-1 [14.9 kB] Get:142 http://ftpmaster.internal/ubuntu artful/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:143 http://ftpmaster.internal/ubuntu artful/main amd64 libhttp-message-perl all 6.11-1 [74.3 kB] Get:144 http://ftpmaster.internal/ubuntu artful/main amd64 libhttp-cookies-perl all 6.01-1 [17.2 kB] Get:145 http://ftpmaster.internal/ubuntu artful/main amd64 libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:146 http://ftpmaster.internal/ubuntu artful/main amd64 libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:147 http://ftpmaster.internal/ubuntu artful/main amd64 libwww-perl all 6.15-2 [135 kB] Get:148 http://ftpmaster.internal/ubuntu artful/main amd64 liblwp-protocol-https-perl all 6.07-2 [8284 B] Get:149 http://ftpmaster.internal/ubuntu artful/universe amd64 libterm-readkey-perl amd64 2.37-1build1 [24.4 kB] Get:150 http://ftpmaster.internal/ubuntu artful/universe amd64 libcpan-uploader-perl all 0.103013-1 [12.9 kB] Get:151 http://ftpmaster.internal/ubuntu artful/universe amd64 libdata-section-perl all 0.200006-1 [12.0 kB] Get:152 http://ftpmaster.internal/ubuntu artful/universe amd64 libclass-inspector-perl all 1.31-1 [16.1 kB] Get:153 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-sharedir-perl all 1.102-2 [11.5 kB] Get:154 http://ftpmaster.internal/ubuntu artful/main amd64 libclass-data-inheritable-perl all 0.08-2 [8774 B] Get:155 http://ftpmaster.internal/ubuntu artful/main amd64 libexception-class-perl all 1.42-1 [25.6 kB] Get:156 http://ftpmaster.internal/ubuntu artful/universe amd64 libscalar-list-utils-perl amd64 1:1.48-1build1 [47.6 kB] Get:157 http://ftpmaster.internal/ubuntu artful/universe amd64 libparams-validationcompiler-perl all 0.24-1 [25.3 kB] Get:158 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-fatal-perl all 0.014-1 [11.1 kB] Get:159 http://ftpmaster.internal/ubuntu artful/universe amd64 libspecio-perl all 0.40-1 [134 kB] Get:160 http://ftpmaster.internal/ubuntu artful/universe amd64 libdatetime-locale-perl all 1:1.16-1 [2168 kB] Get:161 http://ftpmaster.internal/ubuntu artful/universe amd64 libclass-singleton-perl all 1.5-1 [13.0 kB] Get:162 http://ftpmaster.internal/ubuntu artful/universe amd64 libdatetime-timezone-perl all 1:2.13-1+2017b [247 kB] Get:163 http://ftpmaster.internal/ubuntu artful/universe amd64 libdatetime-perl amd64 2:1.43-1 [90.6 kB] Get:164 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-copy-recursive-perl all 0.38-1 [20.6 kB] Get:165 http://ftpmaster.internal/ubuntu artful/main amd64 libnumber-compare-perl all 0.03-1 [7318 B] Get:166 http://ftpmaster.internal/ubuntu artful/main amd64 libtext-glob-perl all 0.10-1 [7554 B] Get:167 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-find-rule-perl all 0.34-1 [28.3 kB] Get:168 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-pushd-perl all 1.014-1 [11.8 kB] Get:169 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-sharedir-install-perl all 0.11-1 [11.8 kB] Get:170 http://ftpmaster.internal/ubuntu artful/universe amd64 libhash-merge-simple-perl all 0.051-1 [7764 B] Get:171 http://ftpmaster.internal/ubuntu artful/universe amd64 libjson-perl all 2.94-1 [73.2 kB] Get:172 http://ftpmaster.internal/ubuntu artful/universe amd64 liblog-dispatch-perl all 2.58-1 [62.3 kB] Get:173 http://ftpmaster.internal/ubuntu artful/universe amd64 liblog-dispatch-array-perl all 1.002-1 [5992 B] Get:174 http://ftpmaster.internal/ubuntu artful/universe amd64 libstring-flogger-perl all 1.101245-1 [6686 B] Get:175 http://ftpmaster.internal/ubuntu artful/universe amd64 libsub-exporter-globexporter-perl all 0.005-1 [7438 B] Get:176 http://ftpmaster.internal/ubuntu artful/universe amd64 liblog-dispatchouli-perl all 2.015-1 [23.8 kB] Get:177 http://ftpmaster.internal/ubuntu artful/main amd64 libexporter-tiny-perl all 0.042-1 [28.8 kB] Get:178 http://ftpmaster.internal/ubuntu artful/main amd64 liblist-moreutils-perl amd64 0.416-1build3 [55.5 kB] Get:179 http://ftpmaster.internal/ubuntu artful/universe amd64 libsyntax-perl all 0.004-1 [6936 B] Get:180 http://ftpmaster.internal/ubuntu artful/universe amd64 libsyntax-keyword-junction-perl all 0.003008-1 [11.7 kB] Get:181 http://ftpmaster.internal/ubuntu artful/universe amd64 libmoose-autobox-perl all 0.16-1 [50.9 kB] Get:182 http://ftpmaster.internal/ubuntu artful/universe amd64 libaliased-perl all 0.34-1 [13.2 kB] Get:183 http://ftpmaster.internal/ubuntu artful/universe amd64 libmoosex-lazyrequire-perl all 0.11-1 [7976 B] Get:184 http://ftpmaster.internal/ubuntu artful/universe amd64 libmoosex-setonce-perl all 0.200002-1 [6716 B] Get:185 http://ftpmaster.internal/ubuntu artful/universe amd64 libcarp-clan-perl all 6.06-1 [11.0 kB] Get:186 http://ftpmaster.internal/ubuntu artful/universe amd64 libsub-exporter-formethods-perl all 0.100052-1 [7346 B] Get:187 http://ftpmaster.internal/ubuntu artful/universe amd64 libmoosex-types-perl all 0.50-1 [49.7 kB] Get:188 http://ftpmaster.internal/ubuntu artful/universe amd64 libmoosex-types-perl-perl all 0.101343-1 [7908 B] Get:189 http://ftpmaster.internal/ubuntu artful/main amd64 libpath-tiny-perl all 0.100-1 [54.3 kB] Get:190 http://ftpmaster.internal/ubuntu artful/universe amd64 libmodule-path-perl all 0.19-1 [11.5 kB] Get:191 http://ftpmaster.internal/ubuntu artful/main amd64 libclone-perl amd64 0.38-2build2 [10.2 kB] Get:192 http://ftpmaster.internal/ubuntu artful/universe amd64 libtask-weaken-perl all 1.04-1 [7628 B] Get:193 http://ftpmaster.internal/ubuntu artful/universe amd64 libppi-perl all 1.236-1 [293 kB] Get:194 http://ftpmaster.internal/ubuntu artful/universe amd64 libperl-prereqscanner-perl all 1.023-1 [32.3 kB] Get:195 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-slurp-tiny-perl all 0.003-1 [6560 B] Get:196 http://ftpmaster.internal/ubuntu artful/universe amd64 libperl-version-perl all 1.013-1 [27.9 kB] Get:197 http://ftpmaster.internal/ubuntu artful/universe amd64 libpod-eventual-perl all 0.094001-1 [13.1 kB] Get:198 http://ftpmaster.internal/ubuntu artful/universe amd64 libtext-template-perl all 1.46-1 [51.5 kB] Get:199 http://ftpmaster.internal/ubuntu artful/universe amd64 libsoftware-license-perl all 0.103012-1 [108 kB] Get:200 http://ftpmaster.internal/ubuntu artful/universe amd64 libterm-encoding-perl all 0.02-1 [5418 B] Get:201 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-deep-perl all 1.127-1 [41.2 kB] Get:202 http://ftpmaster.internal/ubuntu artful/main amd64 libyaml-tiny-perl all 1.70-1 [25.1 kB] Get:203 http://ftpmaster.internal/ubuntu artful/universe amd64 libdist-zilla-perl all 6.010-1 [309 kB] Get:204 http://ftpmaster.internal/ubuntu artful/universe amd64 dh-dist-zilla all 1.3.4 [17.0 kB] Get:205 http://ftpmaster.internal/ubuntu artful/main amd64 libalgorithm-diff-perl all 1.19.03-1 [47.6 kB] Get:206 http://ftpmaster.internal/ubuntu artful/universe amd64 libarray-utils-perl all 0.5-1 [5962 B] Get:207 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libblas-common amd64 3.7.1-1ubuntu4 [5846 B] Get:208 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libblas3 amd64 3.7.1-1ubuntu4 [137 kB] Get:209 http://ftpmaster.internal/ubuntu artful/main amd64 libpixman-1-0 amd64 0.34.0-1 [230 kB] Get:210 http://ftpmaster.internal/ubuntu artful/main amd64 libxcb-render0 amd64 1.11.1-1ubuntu1 [11.4 kB] Get:211 http://ftpmaster.internal/ubuntu artful/main amd64 libxcb-shm0 amd64 1.11.1-1ubuntu1 [5588 B] Get:212 http://ftpmaster.internal/ubuntu artful/main amd64 libcairo2 amd64 1.14.10-1 [557 kB] Get:213 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libcurl3 amd64 7.55.0-1ubuntu1 [195 kB] Get:214 http://ftpmaster.internal/ubuntu artful/main amd64 libdatrie1 amd64 0.2.10-5 [17.6 kB] Get:215 http://ftpmaster.internal/ubuntu artful/universe amd64 libstring-truncate-perl all 1.100602-1 [9730 B] Get:216 http://ftpmaster.internal/ubuntu artful/universe amd64 libpod-elemental-perl all 0.103004-1 [76.1 kB] Get:217 http://ftpmaster.internal/ubuntu artful/universe amd64 libpod-elemental-perlmunger-perl all 0.200006-1 [9260 B] Get:218 http://ftpmaster.internal/ubuntu artful/universe amd64 libpod-weaver-perl all 4.015-1 [61.2 kB] Get:219 http://ftpmaster.internal/ubuntu artful/universe amd64 libdist-zilla-plugin-podweaver-perl all 4.008-1 [7598 B] Get:220 http://ftpmaster.internal/ubuntu artful/universe amd64 libenv-path-perl all 0.19-1 [20.9 kB] Get:221 http://ftpmaster.internal/ubuntu artful/universe amd64 libfile-grep-perl all 0.02-1 [7458 B] Get:222 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libgraph-readwrite-perl all 2.09-1 [42.6 kB] Get:232 http://ftpmaster.internal/ubuntu artful/main amd64 libgraphite2-3 amd64 1.3.10-2 [78.3 kB] Get:233 http://ftpmaster.internal/ubuntu artful/main amd64 libharfbuzz0b amd64 1.4.2-1 [211 kB] Get:234 http://ftpmaster.internal/ubuntu artful/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:235 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 liblapack3 amd64 3.7.1-1ubuntu4 [2113 kB] Get:236 http://ftpmaster.internal/ubuntu artful/universe amd64 liblog-log4perl-perl all 1.49-1 [344 kB] Get:237 http://ftpmaster.internal/ubuntu artful/main amd64 libthai-data all 0.1.26-3 [132 kB] Get:238 http://ftpmaster.internal/ubuntu artful/main amd64 libthai0 amd64 0.1.26-3 [17.7 kB] Get:239 http://ftpmaster.internal/ubuntu artful/main amd64 libpango-1.0-0 amd64 1.40.11-0ubuntu1 [153 kB] Get:240 http://ftpmaster.internal/ubuntu artful/main amd64 libpangoft2-1.0-0 amd64 1.40.11-0ubuntu1 [33.2 kB] Get:241 http://ftpmaster.internal/ubuntu 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kB] Get:251 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-files-perl all 0.14-1 [9138 B] Get:252 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-warn-perl all 0.32-1 [13.6 kB] Get:253 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-most-perl all 0.35-1 [22.1 kB] Get:254 http://ftpmaster.internal/ubuntu artful/universe amd64 libtest-output-perl all 1.031-1 [11.4 kB] Get:255 http://ftpmaster.internal/ubuntu artful/universe amd64 libtext-csv-perl all 1.95-1 [92.7 kB] Get:256 http://ftpmaster.internal/ubuntu artful/main amd64 libtiff5 amd64 4.0.8-4 [150 kB] Get:257 http://ftpmaster.internal/ubuntu artful/main amd64 libtk8.6 amd64 8.6.7-1 [692 kB] Get:258 http://ftpmaster.internal/ubuntu artful/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:259 http://ftpmaster.internal/ubuntu artful/universe amd64 mafft amd64 7.307-1 [906 kB] Get:260 http://ftpmaster.internal/ubuntu artful/universe amd64 ncbi-data all 6.1.20170106-2 [3645 kB] Get:261 http://ftpmaster.internal/ubuntu artful/universe amd64 ncbi-blast+ amd64 2.6.0-1 [9446 kB] Get:262 http://ftpmaster.internal/ubuntu artful/universe amd64 prank amd64 0.0.150803-2 [377 kB] Get:263 http://ftpmaster.internal/ubuntu artful/main amd64 zip amd64 3.0-11build1 [167 kB] Get:264 http://ftpmaster.internal/ubuntu artful/main amd64 unzip amd64 6.0-21ubuntu1 [167 kB] Get:265 http://ftpmaster.internal/ubuntu artful/main amd64 xdg-utils all 1.1.1-1ubuntu2 [59.6 kB] Get:266 http://ftpmaster.internal/ubuntu artful/universe amd64 r-base-core amd64 3.4.1-2 [23.1 MB] Get:267 http://ftpmaster.internal/ubuntu artful/main amd64 sysstat amd64 11.5.7-1 [298 kB] Get:268 http://ftpmaster.internal/ubuntu artful/universe amd64 fasttree amd64 2.1.9-2 [171 kB] Get:269 http://ftpmaster.internal/ubuntu artful/universe amd64 mcl amd64 1:14-137-1 [544 kB] Get:270 http://ftpmaster.internal/ubuntu artful/universe amd64 parallel all 20161222-1 [260 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.0 MB in 5s (15.5 MB/s) (Reading database ... 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Selecting previously unselected package mcl. Preparing to unpack .../235-mcl_1%3a14-137-1_amd64.deb ... Unpacking mcl (1:14-137-1) ... Selecting previously unselected package parallel. Preparing to unpack .../236-parallel_20161222-1_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20161222-1) ... Selecting previously unselected package sbuild-build-depends-roary-dummy. Preparing to unpack .../237-sbuild-build-depends-roary-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-roary-dummy (0.invalid.0) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libpath-tiny-perl (0.100-1) ... Setting up libsub-install-perl (0.928-1) ... Setting up libfindbin-libs-perl (2.150-2) ... Setting up prank (0.0.150803-2) ... Setting up mafft (7.307-1) ... Setting up libtest-deep-perl (1.127-1) ... Setting up libio-stringy-perl (2.111-2) ... Setting up libparse-yapp-perl (1.21-1) ... Setting up cd-hit (4.6.8-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libtry-tiny-perl (0.28-1) ... Setting up libmodule-path-perl (0.19-1) ... Setting up libfile-slurp-tiny-perl (0.003-1) ... Setting up libexpat1:amd64 (2.2.3-1) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up liblog-log4perl-perl (1.49-1) ... Setting up libclass-data-inheritable-perl (0.08-2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up bedtools (2.26.0+dfsg-3) ... Setting up mime-support (3.60ubuntu1) ... Setting up libfile-which-perl (1.21-1) ... Setting up libgfortran4:amd64 (7.2.0-1ubuntu1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libvariable-magic-perl (0.61-1build1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libjbig0:amd64 (2.1-3.1) ... Setting up libsigsegv2:amd64 (2.11-1) ... Setting up librole-tiny-perl (2.000005-1) ... Setting up libcurl3:amd64 (7.55.0-1ubuntu1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libgraph-perl (1:0.96-2) ... Setting up libterm-encoding-perl (0.02-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libblas-common (3.7.1-1ubuntu4) ... Setting up libfile-homedir-perl (1.00-1) ... Setting up libdevel-stacktrace-perl (2.0200-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.53.4-3ubuntu1) ... No schema files found: doing nothing. Setting up libcapture-tiny-perl (0.46-1) ... Setting up libio-html-perl (1.001-1) ... Setting up libexporter-tiny-perl (0.042-1) ... Setting up unzip (6.0-21ubuntu1) ... Setting up libtie-ixhash-perl (1.23-2) ... Setting up libcarp-clan-perl (6.06-1) ... Setting up libperlio-utf8-strict-perl (0.006-1build3) ... Setting up libdatrie1:amd64 (0.2.10-5) ... Setting up gettext-base (0.19.8.1-2ubuntu2) ... Setting up libjpeg-turbo8:amd64 (1.5.1-0ubuntu1) ... Setting up libpipeline1:amd64 (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libarray-utils-perl (0.5-1) ... Setting up libsub-identify-perl (0.12-2build3) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libbsd0:amd64 (0.8.6-1) ... Setting up libyaml-tiny-perl (1.70-1) ... Setting up ucf (3.0036) ... Setting up libxml-writer-perl (0.625-1) ... Setting up libtest-file-perl (1.443-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3.1) ... Setting up zip (3.0-11build1) ... Setting up libterm-readkey-perl (2.37-1build1) ... Setting up libfreetype6:amd64 (2.8-0.2ubuntu1) ... Setting up libmagic-mgc (1:5.31-1) ... Setting up libscope-guard-perl (0.21-1) ... Setting up libmagic1:amd64 (1:5.31-1) ... Setting up libgraphite2-3:amd64 (1.3.10-2) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libfile-pushd-perl (1.014-1) ... Setting up libaliased-perl (0.34-1) ... Setting up libenv-path-perl (0.19-1) ... Setting up libtext-glob-perl (0.10-1) ... Setting up libpackage-stash-xs-perl (0.28-3build2) ... Setting up libstrictures-perl (2.000003-1) ... Setting up ncbi-data (6.1.20170106-2) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libblas3 (3.7.1-1ubuntu4) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libcpanel-json-xs-perl (3.0225-1build1) ... Setting up libautobox-perl (2.85-1build1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libfile-sharedir-install-perl (0.11-1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libjson-maybexs-perl (1.003008-1) ... Setting up fasttree (2.1.9-2) ... Setting up autotools-dev (20161112.1) ... Setting up liburi-perl (1.72-1) ... Setting up libio-tiecombine-perl (1.005-1) ... Setting up libscalar-list-utils-perl (1:1.48-1build1) ... Processing triggers for systemd (234-2ubuntu8) ... Setting up libhtml-parser-perl (3.72-3build1) ... Setting up mcl (1:14-137-1) ... Setting up libfile-grep-perl (0.02-1) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up libio-string-perl (1.08-3) ... Setting up libalgorithm-diff-perl (1.19.03-1) ... Setting up libclone-perl (0.38-2build2) ... Setting up libsensors4:amd64 (1:3.4.0-4) ... Setting up libnet-http-perl (6.16-1) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libtest-fatal-perl (0.014-1) ... Setting up libhash-merge-simple-perl (0.051-1) ... Setting up libtcl8.6:amd64 (8.6.7+dfsg-1) ... Setting up libthai-data (0.1.26-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... 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 libjson-perl (2.94-1) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libparams-util-perl (1.07-3build3) ... Setting up x11-common (1:7.7+19ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1ubuntu2) ... Setting up libsub-name-perl (0.21-1build1) ... Setting up libtext-csv-perl (1.95-1) ... Setting up libparams-classify-perl (0.013-8build1) ... Setting up libsub-quote-perl (2.004000-1) ... Setting up libperl-version-perl (1.013-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libtext-template-perl (1.46-1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-4) ... Setting up libdata-stag-perl (0.14-1ubuntu2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libfile-slurper-perl (0.009-1) ... Setting up autopoint (0.19.8.1-2ubuntu2) ... Setting up libalgorithm-c3-perl (0.10-1) ... Setting up libclass-inspector-perl (1.31-1) ... Setting up libclass-c3-perl (0.32-1) ... Setting up libclass-singleton-perl (1.5-1) ... Setting up libfile-copy-recursive-perl (0.38-1) ... Setting up libspiffy-perl (0.41-1) ... Setting up libmodule-pluggable-perl (5.2-1) ... Setting up libtest-warn-perl (0.32-1) ... Setting up libtask-weaken-perl (1.04-1) ... Setting up netbase (5.4) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up liblist-moreutils-perl (0.416-1build3) ... Setting up libpaper1:amd64 (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up libdata-optlist-perl (0.110-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up fontconfig-config (2.11.94-0ubuntu2) ... Setting up libhttp-date-perl (6.02-1) ... Setting up sysstat (11.5.7-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /lib/systemd/system/sysstat.service. Setting up libppi-perl (1.236-1) ... Setting up libbio-perl-perl (1.7.1-2) ... Setting up libexception-class-perl (1.42-1) ... Setting up gettext (0.19.8.1-2ubuntu2) ... Setting up libnet-ssleay-perl (1.80-1build1) ... Setting up libmodule-runtime-perl (0.014-2) ... Setting up libtest-output-perl (1.031-1) ... Setting up liblapack3 (3.7.1-1ubuntu4) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libtext-diff-perl (1.44-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up python2.7 (2.7.13-4) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up libtiff5:amd64 (4.0.8-4) ... Setting up autoconf (2.69-11) ... Setting up libthai0:amd64 (0.1.26-3) ... Setting up libmro-compat-perl (0.12-1) ... Setting up file (1:5.31-1) ... Setting up libio-socket-ssl-perl (2.050-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libio-all-perl (0.86-2) ... Setting up libsub-exporter-perl (0.986-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libstring-rewriteprefix-perl (0.007-1) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libmixin-linewise-perl (0.108-1) ... Setting up bioperl (1.7.1-2) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhttp-message-perl (6.11-1) ... Setting up libeval-closure-perl (0.14-1) ... Setting up libsub-exporter-formethods-perl (0.100052-1) ... Setting up libparams-validationcompiler-perl (0.24-1) ... Setting up libfile-sharedir-perl (1.102-2) ... Setting up libdist-checkconflicts-perl (0.11-1) ... Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ... Setting up libsub-exporter-globexporter-perl (0.005-1) ... Setting up python (2.7.13-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:amd64 (2.11.94-0ubuntu2) ... Setting up libsm6:amd64 (2:1.2.2-1) ... Setting up parallel (20161222-1) ... Setting up libdata-section-perl (0.200006-1) ... Setting up libconfig-ini-perl (1:0.025-1) ... Setting up libxcb-render0:amd64 (1.11.1-1ubuntu1) ... Setting up libstring-flogger-perl (1.101245-1) ... Setting up libtest-differences-perl (0.64-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libtest-files-perl (0.14-1) ... Setting up po-debconf (1.0.20) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libstring-truncate-perl (1.100602-1) ... Setting up libstring-formatter-perl (0.102084-1) ... Setting up libpod-eventual-perl (0.094001-1) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up libmodule-runtime-conflicts-perl (0.003-1) ... Setting up libstring-errf-perl (0.008-1) ... Setting up libparams-validate-perl (1.29-1) ... Setting up libsoftware-license-perl (0.103012-1) ... Setting up libxcb-shm0:amd64 (1.11.1-1ubuntu1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libmoo-perl (2.003002-1) ... Setting up libspecio-perl (0.40-1) ... Setting up libb-hooks-endofscope-perl (0.21-1) ... Setting up libthrowable-perl (0.200013-1) ... Setting up libxft2:amd64 (2.3.2-1) ... Setting up fontconfig (2.11.94-0ubuntu2) ... Regenerating fonts cache... done. Setting up libtest-most-perl (0.35-1) ... Setting up libpackage-stash-perl (0.37-1) ... Setting up liblog-dispatch-perl (2.58-1) ... Setting up libgetopt-long-descriptive-perl (0.100-1) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up liblog-dispatch-array-perl (1.002-1) ... Setting up libdevel-overloadinfo-perl (0.004-1) ... Setting up libclass-load-perl (0.24-1) ... Setting up libpackage-deprecationmanager-perl (0.17-1) ... Setting up libpango-1.0-0:amd64 (1.40.11-0ubuntu1) ... Setting up libclass-load-xs-perl (0.10-1build1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up libsyntax-perl (0.004-1) ... Setting up libapp-cmd-perl (0.331-1) ... Setting up libnamespace-autoclean-perl (0.28-1) ... Setting up liblog-dispatchouli-perl (2.015-1) ... Setting up libcairo2:amd64 (1.14.10-1) ... Setting up libdatetime-timezone-perl (1:2.13-1+2017b) ... Setting up libsyntax-keyword-junction-perl (0.003008-1) ... Setting up libtk8.6:amd64 (8.6.7-1) ... Setting up libmoose-perl (2.1807-1build1) ... Setting up libdatetime-locale-perl (1:1.16-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.11-0ubuntu1) ... Setting up libperl-prereqscanner-perl (1.023-1) ... Setting up libmoosex-setonce-perl (0.200002-1) ... Setting up libmoosex-role-parameterized-perl (1.09-1) ... Setting up libmoosex-types-perl (0.50-1) ... Setting up libpod-elemental-perl (0.103004-1) ... Setting up librole-hasmessage-perl (0.006-1) ... Setting up libmoose-autobox-perl (0.16-1) ... Setting up librole-identifiable-perl (0.006-1) ... Setting up libmoosex-lazyrequire-perl (0.11-1) ... Setting up libdatetime-perl (2:1.43-1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.11-0ubuntu1) ... Setting up libpod-elemental-perlmunger-perl (0.200006-1) ... Setting up libmoosex-types-perl-perl (0.101343-1) ... Setting up libmoosex-oneargnew-perl (0.003-1) ... Setting up libconfig-mvp-perl (2.200010-1) ... Setting up r-base-core (3.4.1-2) ... Creating config file /etc/R/Renviron with new version Setting up libconfig-mvp-reader-ini-perl (2.101463-1) ... Setting up libpod-weaver-perl (4.015-1) ... Setting up libwww-perl (6.15-2) ... Setting up dh-autoreconf (14) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up libxml-parser-perl (2.44-2build3) ... Setting up libgraph-readwrite-perl (2.09-1) ... Setting up libcpan-uploader-perl (0.103013-1) ... Setting up libdist-zilla-perl (6.010-1) ... Setting up debhelper (10.7.2ubuntu2) ... Setting up dh-dist-zilla (1.3.4) ... Setting up libdist-zilla-plugin-podweaver-perl (4.008-1) ... Setting up sbuild-build-depends-roary-dummy (0.invalid.0) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 29073 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for systemd (234-2ubuntu8) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-92-generic amd64 (x86_64) Toolchain package versions: binutils_2.29-5ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-4ubuntu1 g++-7_7.2.0-1ubuntu1 gcc-6_6.4.0-4ubuntu1 gcc-7_7.2.0-1ubuntu1 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-4ubuntu1 libstdc++-7-dev_7.2.0-1ubuntu1 libstdc++6_7.2.0-1ubuntu1 linux-libc-dev_4.12.0-12.13 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta2 apt-transport-https_1.5~beta2 autoconf_2.69-11 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu2 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 bedtools_2.26.0+dfsg-3 binutils_2.29-5ubuntu1 bioperl_1.7.1-2 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20170717 cd-hit_4.6.8-1 coreutils_8.26-3ubuntu3 cpp_4:7.1.0-1ubuntu3 cpp-6_6.4.0-4ubuntu1 cpp-7_7.2.0-1ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.7.2ubuntu2 debianutils_4.8.2 dh-autoreconf_14 dh-dist-zilla_1.3.4 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-1ubuntu2 fasttree_2.1.9-2 file_1:5.31-1 findutils_4.6.0+git+20170729-2 fontconfig_2.11.94-0ubuntu2 fontconfig-config_2.11.94-0ubuntu2 fonts-dejavu-core_2.37-1 g++_4:7.1.0-1ubuntu3 g++-6_6.4.0-4ubuntu1 g++-7_7.2.0-1ubuntu1 gcc_4:7.1.0-1ubuntu3 gcc-6_6.4.0-4ubuntu1 gcc-6-base_6.4.0-4ubuntu1 gcc-7_7.2.0-1ubuntu1 gcc-7-base_7.2.0-1ubuntu1 gettext_0.19.8.1-2ubuntu2 gettext-base_0.19.8.1-2ubuntu2 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49 init-system-helpers_1.49 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libalgorithm-c3-perl_0.10-1 libalgorithm-diff-perl_1.19.03-1 libaliased-perl_0.34-1 libapp-cmd-perl_0.331-1 libapparmor1_2.11.0-2ubuntu16 libapt-pkg5.0_1.5~beta2 libarchive-zip-perl_1.59-1 libarray-utils-perl_0.5-1 libasan3_6.4.0-4ubuntu1 libasan4_7.2.0-1ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-1ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libautobox-perl_2.85-1build1 libb-hooks-endofscope-perl_0.21-1 libbio-perl-perl_1.7.1-2 libblas-common_3.7.1-1ubuntu4 libblas3_3.7.1-1ubuntu4 libblkid1_2.30.1-0ubuntu3 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12ubuntu1 libc-dev-bin_2.24-12ubuntu1 libc6_2.24-12ubuntu1 libc6-dev_2.24-12ubuntu1 libcairo2_1.14.10-1 libcap-ng0_0.7.7-3build1 libcap2_1:2.25-1 libcapture-tiny-perl_0.46-1 libcarp-clan-perl_6.06-1 libcc1-0_7.2.0-1ubuntu1 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libtsan0_7.2.0-1ubuntu1 libubsan0_7.2.0-1ubuntu1 libudev1_234-2ubuntu8 libunistring0_0.9.3-5.2ubuntu1 liburi-perl_1.72-1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu3 libvariable-magic-perl_0.61-1build1 libwind0-heimdal_7.4.0.dfsg.1-2 libwww-perl_6.15-2 libwww-robotrules-perl_6.01-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb-render0_1.11.1-1ubuntu1 libxcb-shm0_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml-parser-perl_2.44-2build3 libxml-writer-perl_0.625-1 libxml2_2.9.4+dfsg1-3.1 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libyaml-tiny-perl_1.70-1 linux-libc-dev_4.12.0-12.13 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 mafft_7.307-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mcl_1:14-137-1 mime-support_3.60ubuntu1 mount_2.30.1-0ubuntu3 multiarch-support_2.24-12ubuntu1 ncbi-blast+_2.6.0-1 ncbi-data_6.1.20170106-2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 netbase_5.4 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 parallel_20161222-1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.0-5 perl-base_5.26.0-5 perl-modules-5.24_5.24.1-2ubuntu1 perl-modules-5.26_5.26.0-5 perl-openssl-defaults_3 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 prank_0.0.150803-2 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-4 python2.7-minimal_2.7.13-4 r-base-core_3.4.1-2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-roary-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 sysstat_11.5.7-1 systemd_234-2ubuntu8 systemd-sysv_234-2ubuntu8 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 ucf_3.0036 unzip_6.0-21ubuntu1 util-linux_2.30.1-0ubuntu3 x11-common_1:7.7+19ubuntu1 xdg-utils_1.1.1-1ubuntu2 xz-utils_5.2.2-1.3 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Aug 22 14:02:33 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./roary_3.9.1+dfsg-1.dsc dpkg-source: info: extracting roary in roary-3.9.1+dfsg dpkg-source: info: unpacking roary_3.9.1+dfsg.orig.tar.gz dpkg-source: info: unpacking roary_3.9.1+dfsg-1.debian.tar.xz dpkg-source: info: applying rename_R_script.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 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=/<>/roary-3.9.1+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/roary-3.9.1+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.9.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build roary-3.9.1+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with dist-zilla dh_dzil_clean dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build dh build --with dist-zilla dh_update_autotools_config dh_autoreconf debian/rules override_dh_dzil_build make[1]: Entering directory '/<>/roary-3.9.1+dfsg' mv bin/create_pan_genome_plots.R bin/create_pan_genome_plots dh_dzil_build -- [DZ] beginning to build Bio-Roary [DZ] writing Bio-Roary in .build/debian-build [DZ] built in .build/debian-build make[1]: Leaving directory '/<>/roary-3.9.1+dfsg' dh_auto_configure -D .build/debian-build perl -I. Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/<>/roary-3.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/roary-3.9.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build make -j4 make[1]: Entering directory '/<>/roary-3.9.1+dfsg/.build/debian-build' cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp bin/iterative_cdhit blib/script/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome cp bin/roary-unique_genes_per_sample blib/script/roary-unique_genes_per_sample "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-unique_genes_per_sample cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents make[1]: Leaving directory '/<>/roary-3.9.1+dfsg/.build/debian-build' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/roary-3.9.1+dfsg' # pass make[1]: Leaving directory '/<>/roary-3.9.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with dist-zilla dh_testroot dh_prep dh_auto_install -D .build/debian-build make -j4 install DESTDIR=/<>/roary-3.9.1\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>/roary-3.9.1+dfsg/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents Manifying 28 pod documents Manifying 25 pod documents Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/roary.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/pan_genome_post_analysis.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm Installing 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/<>/roary-3.9.1+dfsg/debian/roary/usr/bin/pan_genome_core_alignment Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/roary Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/create_pan_genome_plots Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/roary-query_pan_genome Installing /<>/roary-3.9.1+dfsg/debian/roary/usr/bin/iterative_cdhit make[1]: Leaving directory '/<>/roary-3.9.1+dfsg/.build/debian-build' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing roary (in debian/roary); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/roary/DEBIAN/control, package roary, directory debian/roary pkgstripfiles: Truncating usr/share/doc/roary/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package roary ... pkgstripfiles: No PNG files. dpkg-deb: building package 'roary' in '../roary_3.9.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../roary_3.9.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build roary-3.9.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170822-2310 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ roary_3.9.1+dfsg-1_amd64.changes: --------------------------------- Format: 1.8 Date: Tue, 22 Aug 2017 15:54:18 +0200 Source: roary Binary: roary Architecture: all Version: 3.9.1+dfsg-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: roary - high speed stand alone pan genome pipeline Changes: roary (3.9.1+dfsg-1) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: Set references to registries . [ Sascha Steinbiss ] * New upstream release. Checksums-Sha1: b147fe7eab589089cb7f33e32d63ccfeef2817a1 174842 roary_3.9.1+dfsg-1_all.deb 9e008f6f5f4c67e01b61d0318d0865175c286c92 14280 roary_3.9.1+dfsg-1_amd64.buildinfo Checksums-Sha256: 9b2b7953e0007795af47e3ac3bd53561dc26eef8ab909c7a70b1be6c71d848c7 174842 roary_3.9.1+dfsg-1_all.deb 856008c3313b414726cc78f24150ea3d55ebeebba2aad636e7657e5940ac830f 14280 roary_3.9.1+dfsg-1_amd64.buildinfo Files: 97975f6f39b061f93761a5794b246cb1 174842 science optional roary_3.9.1+dfsg-1_all.deb f237f34ca7d21e95e8e565eb15c16f20 14280 science optional roary_3.9.1+dfsg-1_amd64.buildinfo +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ roary_3.9.1+dfsg-1_all.deb -------------------------- new debian package, version 2.0. size 174842 bytes: control archive=6686 bytes. 1527 bytes, 20 lines control 16815 bytes, 194 lines md5sums Package: roary Version: 3.9.1+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 654 Depends: perl, bioperl, libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Section: science Priority: optional Homepage: http://sanger-pathogens.github.io/Roary/ Description: high speed stand alone pan genome pipeline Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (as produced, for instance, by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes. drwxr-xr-x root/root 0 2017-08-22 13:54 ./ drwxr-xr-x root/root 0 2017-08-22 13:54 ./usr/ drwxr-xr-x root/root 0 2017-08-22 13:54 ./usr/bin/ -rwxr-xr-x root/root 971 2017-08-22 13:54 ./usr/bin/create_pan_genome -rwxr-xr-x root/root 3197 2017-08-22 13:54 ./usr/bin/create_pan_genome_plots -rwxr-xr-x root/root 952 2017-08-22 13:54 ./usr/bin/extract_proteome_from_gff -rwxr-xr-x root/root 841 2017-08-22 13:54 ./usr/bin/iterative_cdhit -rwxr-xr-x root/root 1045 2017-08-22 13:54 ./usr/bin/pan_genome_assembly_statistics -rwxr-xr-x root/root 1159 2017-08-22 13:54 ./usr/bin/pan_genome_core_alignment -rwxr-xr-x root/root 936 2017-08-22 13:54 ./usr/bin/pan_genome_post_analysis -rwxr-xr-x root/root 1044 2017-08-22 13:54 ./usr/bin/pan_genome_reorder_spreadsheet -rwxr-xr-x root/root 1032 2017-08-22 13:54 ./usr/bin/parallel_all_against_all_blastp -rwxr-xr-x root/root 1111 2017-08-22 13:54 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Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 9716 Build-Time: 36 Distribution: artful-proposed Host Architecture: amd64 Install-Time: 41 Job: roary_3.9.1+dfsg-1.dsc Machine Architecture: amd64 Package: roary Package-Time: 79 Source-Version: 3.9.1+dfsg-1 Space: 9716 Status: successful Version: 3.9.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 20170822-2310 Build needed 00:01:19, 9716k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-13283256'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-13283256/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-13283256'] Unmounting chroot for build PACKAGEBUILD-13283256... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-13283256'] Removing build PACKAGEBUILD-13283256