RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 Buildd toolchain package versions: launchpad-buildd_114-0~53~0.IS.08.04 python-lpbuildd_114-0~53~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 5 Nov 11:36:49 ntpdate[18035]: adjust time server 10.211.37.1 offset -0.001019 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '96edd4afb821ac1b001727691d94afb5a48b5f85', '/home/buildd/filecache-default/0e8a5f9bfc531f9cf6b067b18129dc360e4deb27'] Unpacking chroot for build 96edd4afb821ac1b001727691d94afb5a48b5f85 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '96edd4afb821ac1b001727691d94afb5a48b5f85'] Mounting chroot for build 96edd4afb821ac1b001727691d94afb5a48b5f85 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '96edd4afb821ac1b001727691d94afb5a48b5f85', 'deb http://ftpmaster.internal/ubuntu raring main universe', 'deb http://ftpmaster.internal/ubuntu raring-security main universe', 'deb http://ftpmaster.internal/ubuntu raring-updates main universe', 'deb http://ftpmaster.internal/ubuntu raring-proposed main universe'] Overriding sources.list in build-96edd4afb821ac1b001727691d94afb5a48b5f85 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '96edd4afb821ac1b001727691d94afb5a48b5f85', 'i386'] Updating debian chroot for build 96edd4afb821ac1b001727691d94afb5a48b5f85 Ign http://ftpmaster.internal raring InRelease Ign http://ftpmaster.internal raring-security InRelease Ign http://ftpmaster.internal raring-updates InRelease Ign http://ftpmaster.internal raring-proposed InRelease Get:1 http://ftpmaster.internal raring Release.gpg [933 B] Get:2 http://ftpmaster.internal raring-security Release.gpg [933 B] Get:3 http://ftpmaster.internal raring-updates Release.gpg [933 B] Get:4 http://ftpmaster.internal raring-proposed Release.gpg [933 B] Get:5 http://ftpmaster.internal raring Release [49.6 kB] Ign http://archive-team.internal raring InRelease Get:6 http://ftpmaster.internal raring-security Release [49.6 kB] Get:7 http://ftpmaster.internal raring-updates Release [49.6 kB] Ign http://archive-team.internal raring Release.gpg Get:8 http://ftpmaster.internal raring-proposed Release [49.6 kB] Get:9 http://archive-team.internal raring Release [723 B] Get:10 http://ftpmaster.internal raring/main i386 Packages [1137 kB] Get:11 http://archive-team.internal raring/main i386 Packages Ign http://archive-team.internal raring/main Translation-en Get:12 http://ftpmaster.internal raring/universe i386 Packages [5332 kB] Get:13 http://ftpmaster.internal raring/main Translation-en [662 kB] Get:14 http://ftpmaster.internal raring/universe Translation-en [3688 kB] Get:15 http://ftpmaster.internal raring-security/main i386 Packages [14 B] Get:16 http://ftpmaster.internal raring-security/universe i386 Packages [14 B] Get:17 http://ftpmaster.internal raring-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal raring-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal raring-updates/main i386 Packages [14 B] Get:20 http://ftpmaster.internal raring-updates/universe i386 Packages [14 B] Get:21 http://ftpmaster.internal raring-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal raring-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal raring-proposed/main i386 Packages [28.9 kB] Get:24 http://ftpmaster.internal raring-proposed/universe i386 Packages [29.5 kB] Get:25 http://ftpmaster.internal raring-proposed/main Translation-en [9799 B] Get:26 http://ftpmaster.internal raring-proposed/universe Translation-en [20.3 kB] Fetched 11.1 MB in 6s (1721 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: kmod libcap2 libgcc-4.7-dev libkmod2 The following packages will be upgraded: adduser base-files busybox-initramfs cpp-4.7 diffutils dpkg dpkg-dev findutils g++-4.7 gcc-4.7 gcc-4.7-base klibc-utils libc-bin libc-dev-bin libc6 libc6-dev libcurl3-gnutls libdpkg-perl libgcc1 libglib2.0-0 libgmp10 libgomp1 libitm1 libklibc libnih-dbus1 libnih1 libpcre3 libquadmath0 libsasl2-2 libsqlite3-0 libstdc++6 libstdc++6-4.7-dev libusb-0.1-4 lsb-base makedev module-init-tools multiarch-support perl perl-base perl-modules 40 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After this operation, 484 kB disk space will be freed. WARNING: The following packages cannot be authenticated! base-files dpkg diffutils findutils perl perl-base perl-modules libcap2 libnih-dbus1 libnih1 libc6-dev libc-dev-bin libc6 libc-bin libitm1 libgomp1 gcc-4.7-base libgcc1 cpp-4.7 libquadmath0 libgcc-4.7-dev libstdc++6-4.7-dev g++-4.7 gcc-4.7 libstdc++6 libgmp10 libusb-0.1-4 libsqlite3-0 libpcre3 libglib2.0-0 libkmod2 lsb-base module-init-tools kmod libcurl3-gnutls libsasl2-2 multiarch-support adduser busybox-initramfs klibc-utils libklibc makedev dpkg-dev libdpkg-perl Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ raring/main base-files i386 6.12ubuntu1 [63.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ raring/main dpkg i386 1.16.9ubuntu1 [1980 kB] Get:3 http://ftpmaster.internal/ubuntu/ raring/main diffutils i386 1:3.2-7ubuntu1 [199 kB] Get:4 http://ftpmaster.internal/ubuntu/ raring/main findutils i386 4.4.2-5ubuntu1 [317 kB] Get:5 http://ftpmaster.internal/ubuntu/ raring/main perl i386 5.14.2-14 [3705 kB] Get:6 http://ftpmaster.internal/ubuntu/ raring/main perl-base i386 5.14.2-14 [1483 kB] Get:7 http://ftpmaster.internal/ubuntu/ raring/main perl-modules all 5.14.2-14 [3392 kB] Get:8 http://ftpmaster.internal/ubuntu/ raring/main libcap2 i386 1:2.22-1ubuntu4 [12.4 kB] Get:9 http://ftpmaster.internal/ubuntu/ raring/main libnih-dbus1 i386 1.0.3-4ubuntu12 [15.5 kB] Get:10 http://ftpmaster.internal/ubuntu/ raring/main libnih1 i386 1.0.3-4ubuntu12 [53.8 kB] Get:11 http://ftpmaster.internal/ubuntu/ raring/main libc6-dev i386 2.16-0ubuntu3 [5420 kB] Get:12 http://ftpmaster.internal/ubuntu/ raring/main libc-dev-bin i386 2.16-0ubuntu3 [74.0 kB] Get:13 http://ftpmaster.internal/ubuntu/ raring/main libc6 i386 2.16-0ubuntu3 [4022 kB] Get:14 http://ftpmaster.internal/ubuntu/ raring/main libc-bin i386 2.16-0ubuntu3 [1129 kB] Get:15 http://ftpmaster.internal/ubuntu/ raring-proposed/main libitm1 i386 4.7.2-5ubuntu4 [35.5 kB] Get:16 http://ftpmaster.internal/ubuntu/ raring-proposed/main libgomp1 i386 4.7.2-5ubuntu4 [29.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ raring-proposed/main gcc-4.7-base i386 4.7.2-5ubuntu4 [16.3 kB] Get:18 http://ftpmaster.internal/ubuntu/ raring-proposed/main libgcc1 i386 1:4.7.2-5ubuntu4 [53.5 kB] Get:19 http://ftpmaster.internal/ubuntu/ raring-proposed/main cpp-4.7 i386 4.7.2-5ubuntu4 [5210 kB] Get:20 http://ftpmaster.internal/ubuntu/ raring-proposed/main libquadmath0 i386 4.7.2-5ubuntu4 [198 kB] Get:21 http://ftpmaster.internal/ubuntu/ raring-proposed/main libgcc-4.7-dev i386 4.7.2-5ubuntu4 [2642 kB] Get:22 http://ftpmaster.internal/ubuntu/ raring-proposed/main libstdc++6-4.7-dev i386 4.7.2-5ubuntu4 [1737 kB] Get:23 http://ftpmaster.internal/ubuntu/ raring-proposed/main g++-4.7 i386 4.7.2-5ubuntu4 [5633 kB] Get:24 http://ftpmaster.internal/ubuntu/ raring-proposed/main gcc-4.7 i386 4.7.2-5ubuntu4 [5866 kB] Get:25 http://ftpmaster.internal/ubuntu/ raring-proposed/main libstdc++6 i386 4.7.2-5ubuntu4 [336 kB] Get:26 http://ftpmaster.internal/ubuntu/ raring/main libgmp10 i386 2:5.0.5+dfsg-2ubuntu1 [253 kB] Get:27 http://ftpmaster.internal/ubuntu/ raring/main libusb-0.1-4 i386 2:0.1.12-23+nmu1 [17.4 kB] Get:28 http://ftpmaster.internal/ubuntu/ raring/main libsqlite3-0 i386 3.7.14.1-1 [373 kB] Get:29 http://ftpmaster.internal/ubuntu/ raring/main libpcre3 i386 1:8.31-1 [158 kB] Get:30 http://ftpmaster.internal/ubuntu/ raring/main libglib2.0-0 i386 2.34.1-1 [958 kB] Get:31 http://ftpmaster.internal/ubuntu/ raring/main libkmod2 i386 9-2ubuntu3 [46.5 kB] Get:32 http://ftpmaster.internal/ubuntu/ raring/main lsb-base all 4.0-0ubuntu27 [10.3 kB] Get:33 http://ftpmaster.internal/ubuntu/ raring/main module-init-tools all 9-2ubuntu3 [1856 B] Get:34 http://ftpmaster.internal/ubuntu/ raring/main kmod i386 9-2ubuntu3 [60.7 kB] Get:35 http://ftpmaster.internal/ubuntu/ raring/main libcurl3-gnutls i386 7.28.0-2ubuntu2 [246 kB] Get:36 http://ftpmaster.internal/ubuntu/ raring/main libsasl2-2 i386 2.1.25.dfsg1-6 [68.8 kB] Get:37 http://ftpmaster.internal/ubuntu/ raring/main multiarch-support i386 2.16-0ubuntu3 [4480 B] Get:38 http://ftpmaster.internal/ubuntu/ raring/main adduser all 3.113+nmu3ubuntu1 [168 kB] Get:39 http://ftpmaster.internal/ubuntu/ raring/main busybox-initramfs i386 1:1.20.0-7ubuntu2 [189 kB] Get:40 http://ftpmaster.internal/ubuntu/ raring/main klibc-utils i386 2.0.1-3ubuntu1 [187 kB] Get:41 http://ftpmaster.internal/ubuntu/ raring/main libklibc i386 2.0.1-3ubuntu1 [47.6 kB] Get:42 http://ftpmaster.internal/ubuntu/ raring/main makedev all 2.3.1-92ubuntu1 [27.3 kB] Get:43 http://ftpmaster.internal/ubuntu/ raring/main dpkg-dev all 1.16.9ubuntu1 [712 kB] Get:44 http://ftpmaster.internal/ubuntu/ raring/main libdpkg-perl all 1.16.9ubuntu1 [188 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.3 MB in 7s (6339 kB/s) (Reading database ... 12401 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu11 (using .../base-files_6.12ubuntu1_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (6.12ubuntu1) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12403 files and directories currently installed.) Preparing to replace dpkg 1.16.7ubuntu6 (using .../dpkg_1.16.9ubuntu1_i386.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.16.9ubuntu1) ... (Reading database ... 12412 files and directories currently installed.) Preparing to replace diffutils 1:3.2-6ubuntu1 (using .../diffutils_1%3a3.2-7ubuntu1_i386.deb) ... Unpacking replacement diffutils ... Setting up diffutils (1:3.2-7ubuntu1) ... (Reading database ... 12412 files and directories currently installed.) Preparing to replace findutils 4.4.2-4ubuntu2 (using .../findutils_4.4.2-5ubuntu1_i386.deb) ... Unpacking replacement findutils ... Setting up findutils (4.4.2-5ubuntu1) ... (Reading database ... 12412 files and directories currently installed.) Preparing to replace perl 5.14.2-13 (using .../perl_5.14.2-14_i386.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-13 (using .../perl-base_5.14.2-14_i386.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-14) ... (Reading database ... 12408 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-13 (using .../perl-modules_5.14.2-14_all.deb) ... Unpacking replacement perl-modules ... Selecting previously unselected package libcap2:i386. Unpacking libcap2:i386 (from .../libcap2_1%3a2.22-1ubuntu4_i386.deb) ... Setting up libcap2:i386 (1:2.22-1ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12413 files and directories currently installed.) Preparing to replace libnih-dbus1:i386 1.0.3-4ubuntu11 (using .../libnih-dbus1_1.0.3-4ubuntu12_i386.deb) ... Unpacking replacement libnih-dbus1:i386 ... Preparing to replace libnih1:i386 1.0.3-4ubuntu11 (using .../libnih1_1.0.3-4ubuntu12_i386.deb) ... Unpacking replacement libnih1:i386 ... Preparing to replace libc6-dev:i386 2.15-0ubuntu20 (using .../libc6-dev_2.16-0ubuntu3_i386.deb) ... Unpacking replacement libc6-dev:i386 ... Preparing to replace libc-dev-bin 2.15-0ubuntu20 (using .../libc-dev-bin_2.16-0ubuntu3_i386.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6:i386 2.15-0ubuntu20 (using .../libc6_2.16-0ubuntu3_i386.deb) ... Checking for services that may need to be restarted... Checking init scripts... Checking for services that may need to be restarted... Checking init scripts... Nothing to restart. Unpacking replacement libc6:i386 ... Setting up libc6:i386 (2.16-0ubuntu3) ... Checking for services that may need to be restarted... Checking init scripts... Nothing to restart. Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12421 files and directories currently installed.) Preparing to replace libc-bin 2.15-0ubuntu20 (using .../libc-bin_2.16-0ubuntu3_i386.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.16-0ubuntu3) ... Installing new version of config file /etc/gai.conf ... (Reading database ... 12421 files and directories currently installed.) Preparing to replace libitm1:i386 4.7.2-2ubuntu1 (using .../libitm1_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libitm1:i386 ... Preparing to replace libgomp1:i386 4.7.2-2ubuntu1 (using .../libgomp1_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libgomp1:i386 ... Preparing to replace gcc-4.7-base:i386 4.7.2-2ubuntu1 (using .../gcc-4.7-base_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement gcc-4.7-base:i386 ... Setting up gcc-4.7-base:i386 (4.7.2-5ubuntu4) ... (Reading database ... 12421 files and directories currently installed.) Preparing to replace libgcc1:i386 1:4.7.2-2ubuntu1 (using .../libgcc1_1%3a4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libgcc1:i386 ... Setting up libgcc1:i386 (1:4.7.2-5ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12421 files and directories currently installed.) Preparing to replace cpp-4.7 4.7.2-2ubuntu1 (using .../cpp-4.7_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement cpp-4.7 ... Preparing to replace libquadmath0:i386 4.7.2-2ubuntu1 (using .../libquadmath0_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libquadmath0:i386 ... Selecting previously unselected package libgcc-4.7-dev:i386. Unpacking libgcc-4.7-dev:i386 (from .../libgcc-4.7-dev_4.7.2-5ubuntu4_i386.deb) ... Replacing files in old package gcc-4.7 ... Preparing to replace libstdc++6-4.7-dev 4.7.2-2ubuntu1 (using .../libstdc++6-4.7-dev_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libstdc++6-4.7-dev:i386 ... Preparing to replace g++-4.7 4.7.2-2ubuntu1 (using .../g++-4.7_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement g++-4.7 ... Preparing to replace gcc-4.7 4.7.2-2ubuntu1 (using .../gcc-4.7_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace libstdc++6:i386 4.7.2-2ubuntu1 (using .../libstdc++6_4.7.2-5ubuntu4_i386.deb) ... Unpacking replacement libstdc++6:i386 ... Setting up libstdc++6:i386 (4.7.2-5ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12428 files and directories currently installed.) Preparing to replace libgmp10:i386 2:5.0.2+dfsg-2ubuntu2 (using .../libgmp10_2%3a5.0.5+dfsg-2ubuntu1_i386.deb) ... Unpacking replacement libgmp10:i386 ... Preparing to replace libusb-0.1-4:i386 2:0.1.12-23 (using .../libusb-0.1-4_2%3a0.1.12-23+nmu1_i386.deb) ... Unpacking replacement libusb-0.1-4:i386 ... Setting up libusb-0.1-4:i386 (2:0.1.12-23+nmu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12428 files and directories currently installed.) Preparing to replace libsqlite3-0:i386 3.7.13-1 (using .../libsqlite3-0_3.7.14.1-1_i386.deb) ... Unpacking replacement libsqlite3-0:i386 ... Preparing to replace libpcre3:i386 1:8.30-5ubuntu1 (using .../libpcre3_1%3a8.31-1_i386.deb) ... Unpacking replacement libpcre3:i386 ... Preparing to replace libglib2.0-0:i386 2.34.0-1ubuntu1 (using .../libglib2.0-0_2.34.1-1_i386.deb) ... Unpacking replacement libglib2.0-0:i386 ... Selecting previously unselected package libkmod2:i386. Unpacking libkmod2:i386 (from .../libkmod2_9-2ubuntu3_i386.deb) ... Preparing to replace lsb-base 4.0-0ubuntu26 (using .../lsb-base_4.0-0ubuntu27_all.deb) ... Unpacking replacement lsb-base ... Setting up lsb-base (4.0-0ubuntu27) ... (Reading database ... 12433 files and directories currently installed.) Preparing to replace module-init-tools 3.16-1ubuntu6 (using .../module-init-tools_9-2ubuntu3_all.deb) ... Unpacking replacement module-init-tools ... dpkg: warning: unable to delete old directory '/etc/depmod.d': Directory not empty Selecting previously unselected package kmod. Unpacking kmod (from .../kmod_9-2ubuntu3_i386.deb) ... Preparing to replace libcurl3-gnutls:i386 7.27.0-1ubuntu1 (using .../libcurl3-gnutls_7.28.0-2ubuntu2_i386.deb) ... Unpacking replacement libcurl3-gnutls:i386 ... Preparing to replace libsasl2-2:i386 2.1.25.dfsg1-5 (using .../libsasl2-2_2.1.25.dfsg1-6_i386.deb) ... Unpacking replacement libsasl2-2:i386 ... Preparing to replace multiarch-support 2.15-0ubuntu20 (using .../multiarch-support_2.16-0ubuntu3_i386.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.16-0ubuntu3) ... (Reading database ... 12435 files and directories currently installed.) Preparing to replace adduser 3.113+nmu1ubuntu1 (using .../adduser_3.113+nmu3ubuntu1_all.deb) ... Unpacking replacement adduser ... Preparing to replace busybox-initramfs 1:1.19.3-7ubuntu1 (using .../busybox-initramfs_1%3a1.20.0-7ubuntu2_i386.deb) ... Unpacking replacement busybox-initramfs ... Preparing to replace klibc-utils 2.0.1-1ubuntu2 (using .../klibc-utils_2.0.1-3ubuntu1_i386.deb) ... Unpacking replacement klibc-utils ... Preparing to replace libklibc 2.0.1-1ubuntu2 (using .../libklibc_2.0.1-3ubuntu1_i386.deb) ... Unpacking replacement libklibc ... Preparing to replace makedev 2.3.1-91ubuntu2 (using .../makedev_2.3.1-92ubuntu1_all.deb) ... Unpacking replacement makedev ... Preparing to replace dpkg-dev 1.16.7ubuntu6 (using .../dpkg-dev_1.16.9ubuntu1_all.deb) ... Unpacking replacement dpkg-dev ... Preparing to replace libdpkg-perl 1.16.7ubuntu6 (using .../libdpkg-perl_1.16.9ubuntu1_all.deb) ... Unpacking replacement libdpkg-perl ... Setting up libnih1:i386 (1.0.3-4ubuntu12) ... Setting up libnih-dbus1:i386 (1.0.3-4ubuntu12) ... Setting up libc-dev-bin (2.16-0ubuntu3) ... Setting up libc6-dev:i386 (2.16-0ubuntu3) ... Setting up libitm1:i386 (4.7.2-5ubuntu4) ... Setting up libgomp1:i386 (4.7.2-5ubuntu4) ... Setting up libgmp10:i386 (2:5.0.5+dfsg-2ubuntu1) ... Setting up cpp-4.7 (4.7.2-5ubuntu4) ... Setting up libquadmath0:i386 (4.7.2-5ubuntu4) ... Setting up libgcc-4.7-dev:i386 (4.7.2-5ubuntu4) ... Setting up libstdc++6-4.7-dev:i386 (4.7.2-5ubuntu4) ... Setting up gcc-4.7 (4.7.2-5ubuntu4) ... Setting up g++-4.7 (4.7.2-5ubuntu4) ... Setting up libsqlite3-0:i386 (3.7.14.1-1) ... Setting up libpcre3:i386 (1:8.31-1) ... Setting up libglib2.0-0:i386 (2.34.1-1) ... No schema files found: doing nothing. Setting up libkmod2:i386 (9-2ubuntu3) ... Setting up kmod (9-2ubuntu3) ... Setting up module-init-tools (9-2ubuntu3) ... Setting up libcurl3-gnutls:i386 (7.28.0-2ubuntu2) ... Setting up libsasl2-2:i386 (2.1.25.dfsg1-6) ... Setting up adduser (3.113+nmu3ubuntu1) ... Setting up busybox-initramfs (1:1.20.0-7ubuntu2) ... Setting up libklibc (2.0.1-3ubuntu1) ... Setting up klibc-utils (2.0.1-3ubuntu1) ... Setting up makedev (2.3.1-92ubuntu1) ... Setting up perl-modules (5.14.2-14) ... Setting up perl (5.14.2-14) ... Setting up libdpkg-perl (1.16.9ubuntu1) ... Setting up dpkg-dev (1.16.9ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '96edd4afb821ac1b001727691d94afb5a48b5f85', 'i386', 'raring-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=raring-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=universe', 'bedtools_2.17.0-1.dsc'] Initiating build 96edd4afb821ac1b001727691d94afb5a48b5f85 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 i686 Automatic build of bedtools_2.17.0-1 on lamiak by sbuild/i386 1.170.5 Build started at 20121105-1138 ****************************************************************************** bedtools_2.17.0-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: cdbs, debhelper (>= 9), quilt, python, zlib1g-dev Checking for already installed source dependencies... cdbs: missing debhelper: missing quilt: missing python: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install cdbs debhelper quilt python zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils dh-apparmor dh-translations diffstat file gettext gettext-base groff-base html2text intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libgettextpo0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libpipeline1 libsigsegv2 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase po-debconf python-scour python2.7 Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois vacation devscripts dh-make gettext-doc groff libdata-dump-perl libcrypt-ssleay-perl libauthen-ntlm-perl less www-browser libmail-box-perl python-doc python-tk python-rsvg python-cairo python2.7-doc procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur libhtml-format-perl libio-socket-inet6-perl libio-socket-ip-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils cdbs debhelper dh-apparmor dh-translations diffstat file gettext gettext-base groff-base html2text intltool intltool-debian libasprintf0c2 libcroco3 libencode-locale-perl libexpat1 libfile-listing-perl libgettextpo0 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-socket-ssl-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic1 libnet-http-perl libnet-ssleay-perl libpipeline1 libsigsegv2 libunistring0 liburi-perl libwww-perl libwww-robotrules-perl libxml-parser-perl libxml2 m4 man-db mime-support netbase po-debconf python python-scour python2.7 quilt zlib1g-dev 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 12.2 MB of archives. After this operation, 38.0 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 libexpat1 libasprintf0c2 libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 file mime-support netbase bsdmainutils gettext-base groff-base man-db libsigsegv2 m4 autoconf autotools-dev automake html2text gettext intltool-debian po-debconf dh-apparmor debhelper liburi-perl libencode-locale-perl libhttp-date-perl libfile-listing-perl libhtml-tagset-perl libhtml-parser-perl libhtml-tree-perl liblwp-mediatypes-perl libhttp-message-perl libhttp-cookies-perl libhttp-negotiate-perl libnet-ssleay-perl libio-socket-ssl-perl libnet-http-perl liblwp-protocol-https-perl libwww-robotrules-perl libwww-perl libxml-parser-perl intltool dh-translations python2.7 python python-scour cdbs diffstat quilt zlib1g-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ raring/main libmagic1 i386 5.11-2 [173 kB] Get:2 http://ftpmaster.internal/ubuntu/ raring/main libexpat1 i386 2.1.0-1ubuntu1 [129 kB] Get:3 http://ftpmaster.internal/ubuntu/ raring/main libasprintf0c2 i386 0.18.1.1-9ubuntu1 [6612 B] Get:4 http://ftpmaster.internal/ubuntu/ raring/main libpipeline1 i386 1.2.2-1 [26.3 kB] Get:5 http://ftpmaster.internal/ubuntu/ raring/main libxml2 i386 2.8.0+dfsg1-5ubuntu2 [668 kB] Get:6 http://ftpmaster.internal/ubuntu/ raring/main libcroco3 i386 0.6.6-1 [100 kB] Get:7 http://ftpmaster.internal/ubuntu/ raring/main libunistring0 i386 0.9.3-5build1 [430 kB] Get:8 http://ftpmaster.internal/ubuntu/ raring/main libgettextpo0 i386 0.18.1.1-9ubuntu1 [119 kB] Get:9 http://ftpmaster.internal/ubuntu/ raring/main file i386 5.11-2 [18.1 kB] Get:10 http://ftpmaster.internal/ubuntu/ raring/main mime-support all 3.52-1ubuntu1 [31.3 kB] Get:11 http://ftpmaster.internal/ubuntu/ raring/main netbase all 5.0ubuntu1 [13.8 kB] Get:12 http://ftpmaster.internal/ubuntu/ raring/main bsdmainutils i386 9.0.3ubuntu1 [197 kB] Get:13 http://ftpmaster.internal/ubuntu/ raring/main gettext-base i386 0.18.1.1-9ubuntu1 [54.8 kB] Get:14 http://ftpmaster.internal/ubuntu/ raring/main groff-base i386 1.21-9 [1028 kB] Get:15 http://ftpmaster.internal/ubuntu/ raring/main man-db i386 2.6.3-1 [749 kB] Get:16 http://ftpmaster.internal/ubuntu/ raring/main libsigsegv2 i386 2.9-4ubuntu3 [14.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ raring/main m4 i386 1.4.16-4ubuntu1 [199 kB] Get:18 http://ftpmaster.internal/ubuntu/ raring/main autoconf all 2.69-1ubuntu1 [568 kB] Get:19 http://ftpmaster.internal/ubuntu/ raring/main autotools-dev all 20120608.1 [42.9 kB] Get:20 http://ftpmaster.internal/ubuntu/ raring/main automake all 1:1.11.6-1ubuntu1 [578 kB] Get:21 http://ftpmaster.internal/ubuntu/ raring/main html2text i386 1.3.2a-15build1 [91.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ raring/main gettext i386 0.18.1.1-9ubuntu1 [1139 kB] Get:23 http://ftpmaster.internal/ubuntu/ raring/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ raring/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:25 http://ftpmaster.internal/ubuntu/ raring/main dh-apparmor all 2.8.0-0ubuntu6 [9688 B] Get:26 http://ftpmaster.internal/ubuntu/ raring/main debhelper all 9.20120608ubuntu1 [623 kB] Get:27 http://ftpmaster.internal/ubuntu/ raring/main liburi-perl all 1.60-1 [89.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ raring/main libencode-locale-perl all 1.03-1 [12.4 kB] Get:29 http://ftpmaster.internal/ubuntu/ raring/main libhttp-date-perl all 6.02-1 [10.4 kB] Get:30 http://ftpmaster.internal/ubuntu/ raring/main libfile-listing-perl all 6.04-1 [9774 B] Get:31 http://ftpmaster.internal/ubuntu/ raring/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:32 http://ftpmaster.internal/ubuntu/ raring/main libhtml-parser-perl i386 3.69-2 [99.4 kB] Get:33 http://ftpmaster.internal/ubuntu/ raring/main libhtml-tree-perl all 5.02-1 [213 kB] Get:34 http://ftpmaster.internal/ubuntu/ raring/main liblwp-mediatypes-perl all 6.02-1 [21.7 kB] Get:35 http://ftpmaster.internal/ubuntu/ raring/main libhttp-message-perl all 6.03-1 [77.6 kB] Get:36 http://ftpmaster.internal/ubuntu/ raring/main libhttp-cookies-perl all 6.00-2 [23.3 kB] Get:37 http://ftpmaster.internal/ubuntu/ raring/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:38 http://ftpmaster.internal/ubuntu/ raring/main libnet-ssleay-perl i386 1.48-1 [313 kB] Get:39 http://ftpmaster.internal/ubuntu/ raring/main libio-socket-ssl-perl all 1.76-1ubuntu1 [51.2 kB] Get:40 http://ftpmaster.internal/ubuntu/ raring/main libnet-http-perl all 6.03-2 [24.0 kB] Get:41 http://ftpmaster.internal/ubuntu/ raring/main liblwp-protocol-https-perl all 6.03-1 [7178 B] Get:42 http://ftpmaster.internal/ubuntu/ raring/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:43 http://ftpmaster.internal/ubuntu/ raring/main libwww-perl all 6.04-1 [156 kB] Get:44 http://ftpmaster.internal/ubuntu/ raring/main libxml-parser-perl i386 2.41-1build2 [278 kB] Get:45 http://ftpmaster.internal/ubuntu/ raring/main intltool all 0.50.2-2 [52.0 kB] Get:46 http://ftpmaster.internal/ubuntu/ raring/main dh-translations all 117 [21.7 kB] Get:47 http://ftpmaster.internal/ubuntu/ raring/main python2.7 i386 2.7.3-5ubuntu4 [2682 kB] Get:48 http://ftpmaster.internal/ubuntu/ raring/main python i386 2.7.3-0ubuntu7 [168 kB] Get:49 http://ftpmaster.internal/ubuntu/ raring/main python-scour all 0.26-3 [46.5 kB] Get:50 http://ftpmaster.internal/ubuntu/ raring/main cdbs all 0.4.118ubuntu1 [48.2 kB] Get:51 http://ftpmaster.internal/ubuntu/ raring/main diffstat i386 1.55-3 [22.9 kB] Get:52 http://ftpmaster.internal/ubuntu/ raring/main quilt all 0.60-2 [285 kB] Get:53 http://ftpmaster.internal/ubuntu/ raring/main zlib1g-dev i386 1:1.2.7.dfsg-13 [177 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.2 MB in 2s (4782 kB/s) Selecting previously unselected package libmagic1:i386. (Reading database ... 12481 files and directories currently installed.) Unpacking libmagic1:i386 (from .../libmagic1_5.11-2_i386.deb) ... Selecting previously unselected package libexpat1:i386. Unpacking libexpat1:i386 (from .../libexpat1_2.1.0-1ubuntu1_i386.deb) ... Selecting previously unselected package libasprintf0c2:i386. Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-9ubuntu1_i386.deb) ... Selecting previously unselected package libpipeline1:i386. Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.2-1_i386.deb) ... Selecting previously unselected package libxml2:i386. Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-5ubuntu2_i386.deb) ... Selecting previously unselected package libcroco3:i386. Unpacking libcroco3:i386 (from .../libcroco3_0.6.6-1_i386.deb) ... Selecting previously unselected package libunistring0:i386. Unpacking libunistring0:i386 (from .../libunistring0_0.9.3-5build1_i386.deb) ... 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Selecting previously unselected package intltool. Unpacking intltool (from .../intltool_0.50.2-2_all.deb) ... Selecting previously unselected package dh-translations. Unpacking dh-translations (from .../dh-translations_117_all.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-5ubuntu4_i386.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-0ubuntu7_i386.deb) ... Selecting previously unselected package python-scour. Unpacking python-scour (from .../python-scour_0.26-3_all.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../cdbs_0.4.118ubuntu1_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-3_i386.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package zlib1g-dev:i386. Unpacking zlib1g-dev:i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_i386.deb) ... Setting up libmagic1:i386 (5.11-2) ... Setting up libexpat1:i386 (2.1.0-1ubuntu1) ... Setting up libasprintf0c2:i386 (0.18.1.1-9ubuntu1) ... Setting up libpipeline1:i386 (1.2.2-1) ... Setting up libxml2:i386 (2.8.0+dfsg1-5ubuntu2) ... Setting up libcroco3:i386 (0.6.6-1) ... Setting up libunistring0:i386 (0.9.3-5build1) ... Setting up libgettextpo0:i386 (0.18.1.1-9ubuntu1) ... Setting up file (5.11-2) ... Setting up mime-support (3.52-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up netbase (5.0ubuntu1) ... Setting up bsdmainutils (9.0.3ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up gettext-base (0.18.1.1-9ubuntu1) ... Setting up groff-base (1.21-9) ... Setting up man-db (2.6.3-1) ... Building database of manual pages ... Setting up libsigsegv2 (2.9-4ubuntu3) ... Setting up m4 (1.4.16-4ubuntu1) ... Setting up autoconf (2.69-1ubuntu1) ... Setting up autotools-dev (20120608.1) ... Setting up automake (1:1.11.6-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode Setting up html2text (1.3.2a-15build1) ... Setting up gettext (0.18.1.1-9ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.8.0-0ubuntu6) ... Setting up debhelper (9.20120608ubuntu1) ... Setting up liburi-perl (1.60-1) ... Setting up libencode-locale-perl (1.03-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.69-2) ... Setting up libhtml-tree-perl (5.02-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.03-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.48-1) ... Setting up libio-socket-ssl-perl (1.76-1ubuntu1) ... Setting up libnet-http-perl (6.03-2) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up python2.7 (2.7.3-5ubuntu4) ... Setting up python (2.7.3-0ubuntu7) ... Setting up python-scour (0.26-3) ... Setting up diffstat (1.55-3) ... Setting up quilt (0.60-2) ... Setting up zlib1g-dev:i386 (1:1.2.7.dfsg-13) ... Setting up liblwp-protocol-https-perl (6.03-1) ... Setting up libwww-perl (6.04-1) ... Setting up libxml-parser-perl (2.41-1build2) ... Setting up intltool (0.50.2-2) ... Setting up dh-translations (117) ... Setting up cdbs (0.4.118ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.16-0ubuntu3 make_3.81-8.2ubuntu2 dpkg-dev_1.16.9ubuntu1 gcc-4.7_4.7.2-5ubuntu4 g++-4.7_4.7.2-5ubuntu4 binutils_2.22.90.20120924-0ubuntu2 libstdc++6-4.7-dev_4.7.2-5ubuntu4 libstdc++6_4.7.2-5ubuntu4 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc dpkg-source: info: extracting bedtools in bedtools-2.17.0 dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz dpkg-source: info: applying gzstream.h.patch dpkg-buildpackage: source package bedtools dpkg-buildpackage: source version 2.17.0-1 dpkg-source --before-build bedtools-2.17.0 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" -k clean make[1]: Entering directory `/build/buildd/bedtools-2.17.0' * Cleaning-up BamTools API * Cleaning up. make[1]: Leaving directory `/build/buildd/bedtools-2.17.0' dh_clean rm -f debian/bedtools.substvars rm -f debian/bedtools.*.debhelper rm -rf debian/bedtools/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/bedtools-2.17.0' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/bedtools-2.17.0' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/build/buildd/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch gzstream.h.patch Restoring src/utils/gzstream/gzstream.C No patches applied rm -rf ./.pc rm -f debian/stamp-patch* debian/rules build test -x debian/rules mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/bedtools-2.17.0' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/bedtools-2.17.0' cd . && QUILT_PATCHES=/build/buildd/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch gzstream.h.patch patching file src/utils/gzstream/gzstream.C Now at patch gzstream.h.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/build/buildd/bedtools-2.17.0' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/build/buildd/bedtools-2.17.0' /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" make[1]: Entering directory `/build/buildd/bedtools-2.17.0' Building BEDTools: ========================================================= DETECTED_VERSION = v2.17.0 CURRENT_VERSION = Updating version file. * Creating BamTools API - Building in src/utils/bedFile * compiling bedFile.cpp - Building in src/utils/version * compiling version.cpp - Building in src/utils/bedGraphFile * compiling bedGraphFile.cpp - Building in src/utils/chromsweep * compiling chromsweep.cpp - Building in src/utils/gzstream g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I. - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/utils/tabFile * compiling tabFile.cpp - Building in src/utils/BamTools * compiling BamAlignment.cpp * compiling BamMultiReader.cpp * compiling BamReader.cpp * compiling BamWriter.cpp * compiling SamHeader.cpp * compiling SamProgram.cpp * compiling SamProgramChain.cpp * compiling SamReadGroup.cpp * compiling SamReadGroupDictionary.cpp * compiling SamSequence.cpp * compiling SamSequenceDictionary.cpp * compiling BamHeader_p.cpp * compiling BamMultiReader_p.cpp * compiling BamRandomAccessController_p.cpp * compiling BamReader_p.cpp * compiling BamWriter_p.cpp * compiling BamIndexFactory_p.cpp * compiling BamStandardIndex_p.cpp * compiling BamToolsIndex_p.cpp * compiling BamDeviceFactory_p.cpp * compiling BamFile_p.cpp * compiling BamFtp_p.cpp * compiling BamHttp_p.cpp * compiling BamPipe_p.cpp * compiling BgzfStream_p.cpp * compiling ByteArray_p.cpp * compiling HostAddress_p.cpp * compiling HostInfo_p.cpp * compiling HttpHeader_p.cpp * compiling ILocalIODevice_p.cpp * compiling RollingBuffer_p.cpp * compiling TcpSocketEngine_p.cpp * compiling TcpSocketEngine_unix_p.cpp * compiling TcpSocket_p.cpp * compiling SamFormatParser_p.cpp * compiling SamFormatPrinter_p.cpp * compiling SamHeaderValidator_p.cpp * compiling BamException_p.cpp * linking lib/libbamtools.a ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o ranlib lib/libbamtools.a - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp * compiling BlockedIntervals.cpp - Building in src/utils/Fasta * compiling Fasta.cpp Fasta.cpp: In member function 'void FastaIndexEntry::clear()': Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)': Fasta.cpp:316:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)': Fasta.cpp:274:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] * compiling Fasta.cpp Fasta.cpp: In member function 'void FastaIndexEntry::clear()': Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)': Fasta.cpp:316:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)': Fasta.cpp:274:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] * compiling split.cpp * compiling split.cpp - Building in src/utils/VectorOps * compiling VectorOps.cpp - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': genomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] - Building in src/annotateBed * compiling annotateMain.cpp annotateMain.cpp: In function 'int annotate_main(int, char**)': annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable] * compiling annotateBed.cpp - Building in src/bamToBed * compiling bamToBed.cpp bamToBed.cpp: In function 'int bamtobed_main(int, char**)': bamToBed.cpp:85:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] - Building in src/bamToFastq * compiling bamToFastqMain.cpp bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] * compiling bamToFastq.cpp - Building in src/bedToBam * compiling bedToBam.cpp bedToBam.cpp: In function 'int bedtobam_main(int, char**)': bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] - Building in src/bedpeToBam * compiling bedpeToBam.cpp bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] - Building in src/bedToIgv * compiling bedToIgv.cpp - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp - Building in src/closestBed * compiling closestMain.cpp * compiling closestBed.cpp - Building in src/clusterBed * compiling clusterMain.cpp clusterMain.cpp: In function 'int cluster_main(int, char**)': clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] * compiling clusterBed.cpp - Building in src/complementBed * compiling complementMain.cpp * compiling complementBed.cpp - Building in src/coverageBed * compiling coverageMain.cpp * compiling coverageBed.cpp - Building in src/expand * compiling expand.cpp - Building in src/fastaFromBed * compiling fastaFromBedMain.cpp * compiling fastaFromBed.cpp - Building in src/flankBed * compiling flankBedMain.cpp * compiling flankBed.cpp - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp * compiling genomeCoverageBed.cpp - Building in src/getOverlap * compiling getOverlap.cpp getOverlap.cpp: In function 'int getoverlap_main(int, char**)': getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] - Building in src/groupBy * compiling groupBy.cpp groupBy.cpp: In function 'int groupby_main(int, char**)': groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable] - Building in src/intersectBed * compiling intersectMain.cpp * compiling intersectBed.cpp - Building in src/jaccard * compiling jaccardMain.cpp * compiling jaccard.cpp - Building in src/linksBed * compiling linksMain.cpp * compiling linksBed.cpp - Building in src/maskFastaFromBed * compiling maskFastaFromBedMain.cpp * compiling maskFastaFromBed.cpp - Building in src/mapBed * compiling mapMain.cpp mapMain.cpp: In function 'int map_main(int, char**)': mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable] mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable] * compiling mapBed.cpp - Building in src/mergeBed * compiling mergeMain.cpp mergeMain.cpp: In function 'int merge_main(int, char**)': mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] * compiling mergeBed.cpp - Building in src/multiBamCov * compiling multiBamCovMain.cpp multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] * compiling multiBamCov.cpp - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] * compiling multiIntersectBed.cpp - Building in src/nucBed * compiling nucBedMain.cpp * compiling nucBed.cpp - Building in src/pairToBed * compiling pairToBedMain.cpp pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] * compiling pairToBed.cpp pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] - Building in src/pairToPair * compiling pairToPairMain.cpp pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] * compiling pairToPair.cpp pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)': pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] - Building in src/randomBed * compiling randomBedMain.cpp * compiling randomBed.cpp - Building in src/shuffleBed * compiling shuffleBedMain.cpp * compiling shuffleBed.cpp - Building in src/slopBed * compiling slopBedMain.cpp * compiling slopBed.cpp - Building in src/sortBed * compiling sortMain.cpp * compiling sortBed.cpp - Building in src/subtractBed * compiling subtractMain.cpp subtractMain.cpp: In function 'int subtract_main(int, char**)': subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] * compiling subtractBed.cpp - Building in src/tagBam * compiling tagBamMain.cpp tagBamMain.cpp: In function 'int tagbam_main(int, char**)': tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] * compiling tagBam.cpp - Building in src/unionBedGraphs * compiling unionBedGraphsMain.cpp unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] * compiling unionBedGraphs.cpp - Building in src/windowBed * compiling windowMain.cpp * compiling windowBed.cpp - Building in src/windowMaker * compiling windowMakerMain.cpp * compiling windowMaker.cpp - Building main bedtools binary. done. - Creating executables for old CLI. done. make[1]: Leaving directory `/build/buildd/bedtools-2.17.0' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks /usr/bin/fakeroot debian/rules binary test -x debian/rules dh_testroot dh_prep rm -f debian/bedtools.substvars rm -f debian/bedtools.*.debhelper rm -rf debian/bedtools/ dh_installdirs -A install -d debian/bedtools mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable DEB_MAKE_CHECK_TARGET unset, not running checks DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target Adding cdbs dependencies to debian/bedtools.substvars dh_installdirs -pbedtools dh_installdocs -pbedtools install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools cp -a README.rst debian/bedtools/usr/share/doc/bedtools chown -R 0:0 debian/bedtools/usr/share/doc chmod -R go=rX debian/bedtools/usr/share/doc chmod -R u\+rw debian/bedtools/usr/share/doc install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright dh_installexamples -pbedtools dh_installman -pbedtools dh_installinfo -pbedtools dh_installmenu -pbedtools dh_installcron -pbedtools dh_installinit -pbedtools dh_installdebconf -pbedtools install -o 0 -g 0 -d debian/bedtools/DEBIAN dh_installemacsen -pbedtools dh_installcatalogs -pbedtools grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true mv debian/bedtools.substvars.new debian/bedtools.substvars dh_installpam -pbedtools dh_installlogrotate -pbedtools dh_installlogcheck -pbedtools dh_installchangelogs -pbedtools RELEASE_HISTORY install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog dh_installudev -pbedtools dh_lintian -pbedtools dh_bugfiles -pbedtools dh_install -pbedtools install -d debian/bedtools/usr/bin cp -a ./bin/annotateBed debian/bedtools/usr/bin/ cp -a ./bin/bamToBed debian/bedtools/usr/bin/ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/ cp -a ./bin/bedToBam debian/bedtools/usr/bin/ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/ cp -a ./bin/bedtools debian/bedtools/usr/bin/ cp -a ./bin/closestBed debian/bedtools/usr/bin/ cp -a ./bin/clusterBed debian/bedtools/usr/bin/ cp -a ./bin/complementBed debian/bedtools/usr/bin/ cp -a ./bin/coverageBed debian/bedtools/usr/bin/ cp -a ./bin/expandCols debian/bedtools/usr/bin/ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/ cp -a ./bin/flankBed debian/bedtools/usr/bin/ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/ cp -a ./bin/getOverlap debian/bedtools/usr/bin/ cp -a ./bin/groupBy debian/bedtools/usr/bin/ cp -a ./bin/intersectBed debian/bedtools/usr/bin/ cp -a ./bin/linksBed debian/bedtools/usr/bin/ cp -a ./bin/mapBed debian/bedtools/usr/bin/ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/ cp -a ./bin/mergeBed debian/bedtools/usr/bin/ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/ cp -a ./bin/nucBed debian/bedtools/usr/bin/ cp -a ./bin/pairToBed debian/bedtools/usr/bin/ cp -a ./bin/pairToPair debian/bedtools/usr/bin/ cp -a ./bin/randomBed debian/bedtools/usr/bin/ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/ cp -a ./bin/slopBed debian/bedtools/usr/bin/ cp -a ./bin/sortBed debian/bedtools/usr/bin/ cp -a ./bin/subtractBed debian/bedtools/usr/bin/ cp -a ./bin/tagBam debian/bedtools/usr/bin/ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/ cp -a ./bin/windowBed debian/bedtools/usr/bin/ cp -a ./bin/windowMaker debian/bedtools/usr/bin/ install -d debian/bedtools/usr/share/bedtools cp -a ./genomes debian/bedtools/usr/share/bedtools/ install -d debian/bedtools/usr/share/bedtools/test cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/ install -d debian/bedtools/etc/bash_completion.d cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/ dh_link -pbedtools dh_installmime -pbedtools dh_installgsettings -pbedtools dh_strip -pbedtools dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: bedtools dh_strip debug symbol extraction: packages to act on: bedtools dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: building package `bedtools-dbgsym' in `../bedtools-dbgsym_2.17.0-1_i386.ddeb'. strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools dh_compress -pbedtools -X test cd debian/bedtools chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog cd '/build/buildd/bedtools-2.17.0' dh_fixperms -pbedtools find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_makeshlibs -pbedtools rm -f debian/bedtools/DEBIAN/shlibs rm /build/buildd/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package. dh_installdeb -pbedtools find debian/bedtools/etc -type f -printf '/etc/%P ' >> debian/bedtools/DEBIAN/conffiles chmod 644 debian/bedtools/DEBIAN/conffiles dh_perl -pbedtools dh_shlibdeps -pbedtools dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_gencontrol -pbedtools echo misc:Depends= >> debian/bedtools.substvars dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/bedtools/DEBIAN/control chown 0:0 debian/bedtools/DEBIAN/control # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -pbedtools ; fi dh_md5sums -pbedtools (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/bedtools/DEBIAN/md5sums chown 0:0 debian/bedtools/DEBIAN/md5sums dh_builddeb -pbedtools -- -Z xz dpkg-deb -Z xz --build debian/bedtools .. INFO: pkgstriptranslations version 117 pkgstriptranslations: processing bedtools (in debian/bedtools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bedtools/DEBIAN/control, package bedtools, directory debian/bedtools .. removing usr/share/doc/bedtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/bedtools/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package bedtools took 0 s dpkg-deb: warning: 'debian/bedtools/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_i386.deb'. dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../bedtools_2.17.0-1_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build bedtools-2.17.0 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20121105-1141 Publishing debug debs. chroot-autobuild/build/buildd/bedtools_2.17.0-1_i386.deb: new debian package, version 2.0. size 435670 bytes: control archive= 4125 bytes. 32 bytes, 1 lines conffiles 912 bytes, 19 lines control 9535 bytes, 131 lines md5sums Package: bedtools Version: 2.17.0-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1532 Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4) Suggests: filo Section: science Priority: optional Homepage: http://code.google.com/p/bedtools/ Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distribued in the filo package. chroot-autobuild/build/buildd/bedtools_2.17.0-1_i386.deb: drwxr-xr-x root/root 0 2012-11-05 11:41 ./ drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/ drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/bin/ -rwxr-xr-x root/root 43 2012-11-05 11:41 ./usr/bin/complementBed -rwxr-xr-x root/root 43 2012-11-05 11:41 ./usr/bin/multiIntersectBed -rwxr-xr-x root/root 37 2012-11-05 11:41 ./usr/bin/sortBed -rwxr-xr-x root/root 38 2012-11-05 11:41 ./usr/bin/flankBed -rwxr-xr-x root/root 42 2012-11-05 11:41 ./usr/bin/genomeCoverageBed -rwxr-xr-x root/root 40 2012-11-05 11:41 ./usr/bin/clusterBed -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/multiBamCov -rwxr-xr-x root/root 36 2012-11-05 11:41 ./usr/bin/bedToIgv -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/coverageBed -rwxr-xr-x root/root 44 2012-11-05 11:41 ./usr/bin/windowMaker -rwxr-xr-x root/root 40 2012-11-05 11:41 ./usr/bin/shuffleBed -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/annotateBed -rwxr-xr-x root/root 38 2012-11-05 11:41 ./usr/bin/mergeBed -rwxr-xr-x root/root 44 2012-11-05 11:41 ./usr/bin/bed12ToBed6 -rwxr-xr-x root/root 42 2012-11-05 11:41 ./usr/bin/intersectBed -rwxr-xr-x root/root 39 2012-11-05 11:41 ./usr/bin/windowBed -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/subtractBed -rwxr-xr-x root/root 43 2012-11-05 11:41 ./usr/bin/pairToPair -rwxr-xr-x root/root 40 2012-11-05 11:41 ./usr/bin/closestBed -rwxr-xr-x root/root 1362176 2012-11-05 11:41 ./usr/bin/bedtools -rwxr-xr-x root/root 36 2012-11-05 11:41 ./usr/bin/tagBam -rwxr-xr-x root/root 36 2012-11-05 11:41 ./usr/bin/nucBed -rwxr-xr-x root/root 42 2012-11-05 11:41 ./usr/bin/unionBedGraphs -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/bamToBed -rwxr-xr-x root/root 43 2012-11-05 11:41 ./usr/bin/bedpeToBam -rwxr-xr-x root/root 42 2012-11-05 11:41 ./usr/bin/maskFastaFromBed -rwxr-xr-x root/root 39 2012-11-05 11:41 ./usr/bin/randomBed -rwxr-xr-x root/root 39 2012-11-05 11:41 ./usr/bin/expandCols -rwxr-xr-x root/root 38 2012-11-05 11:41 ./usr/bin/linksBed -rwxr-xr-x root/root 43 2012-11-05 11:41 ./usr/bin/bamToFastq -rwxr-xr-x root/root 36 2012-11-05 11:41 ./usr/bin/mapBed -rwxr-xr-x root/root 42 2012-11-05 11:41 ./usr/bin/pairToBed -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/fastaFromBed -rwxr-xr-x root/root 37 2012-11-05 11:41 ./usr/bin/slopBed -rwxr-xr-x root/root 40 2012-11-05 11:41 ./usr/bin/getOverlap -rwxr-xr-x root/root 41 2012-11-05 11:41 ./usr/bin/bedToBam drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/share/ drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/share/bedtools/ drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/share/bedtools/test/ drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/closest/ -rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed -rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh -rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed -rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed -rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed -rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/subtract/ -rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed -rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh -rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/expand/ -rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh -rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/coverage/ -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai -rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed -rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam -rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed -rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam -rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai -rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/intersect/ -rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam -rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed -rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam -rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed -rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed -rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh -rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed -rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam -rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/groupBy/ -rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh -rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/genomecov/ -rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed -rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam -rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh -rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed -rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed -rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam -rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/getfasta/ -rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai -rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed -rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa -rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed -rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/jaccard/ -rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh -rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed -rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed -rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed -rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/bamtobed/ -rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam -rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam -rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh -rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/bed12tobed6/ -rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed -rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed -rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed -rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh -rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed -rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/flank/ -rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed -rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh -rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/merge/ -rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed -rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh -rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed -rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/slop/ -rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed -rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh -rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/map/ -rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed -rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed -rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh -rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed -rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/multicov/ -rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam -rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai -rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh -rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai -rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/cluster/ -rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed -rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/test/general/ -rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh drwxr-xr-x root/root 0 2012-11-05 11:39 ./usr/share/bedtools/genomes/ -rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome -rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome -rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome -rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-11-05 11:41 ./usr/share/doc/bedtools/ -rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright -rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst -rw-r--r-- root/root 903 2012-11-05 11:41 ./usr/share/doc/bedtools/changelog.Debian.gz drwxr-xr-x root/root 0 2012-11-05 11:41 ./etc/ drwxr-xr-x root/root 0 2012-11-05 11:41 ./etc/bash_completion.d/ -rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools bedtools_2.17.0-1_i386.changes: Format: 1.8 Date: Sun, 04 Nov 2012 17:59:41 +0900 Source: bedtools Binary: bedtools Architecture: i386 Version: 2.17.0-1 Distribution: raring-proposed Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Charles Plessy Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.17.0-1) unstable; urgency=low . bb9012e Imported Upstream version 2.16.2. 9006b23 Imported Upstream version 2.17.0. 9112569 Documented BEDTools license as a whole. 325689c Removed Pre-Depends: dpkg (>= 1.15.6). a781b14 Conforms with Policy 3.9.4. 84b1167 Use Debhelper 9. 0bf572d Distribute the test suite. 422cd34 Bash completion for BEDTools. Checksums-Sha1: 4b39552f55af9bcaafffd8d1625cbda0b4477024 435670 bedtools_2.17.0-1_i386.deb Checksums-Sha256: 8abf5349d4211e18489d2aeff7cfcf36d5a81f9d035365450ac7a96917fde832 435670 bedtools_2.17.0-1_i386.deb Files: b2f515abdd943c17d75d1390ee668dd8 435670 science optional bedtools_2.17.0-1_i386.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20121105-1141 Build needed 00:02:30, 74560k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '96edd4afb821ac1b001727691d94afb5a48b5f85'] Scanning for processes to kill in build /home/buildd/build-96edd4afb821ac1b001727691d94afb5a48b5f85/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '96edd4afb821ac1b001727691d94afb5a48b5f85'] Unmounting chroot for build 96edd4afb821ac1b001727691d94afb5a48b5f85... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '96edd4afb821ac1b001727691d94afb5a48b5f85'] Removing build 96edd4afb821ac1b001727691d94afb5a48b5f85