RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.38-1209-omap4 #21-Ubuntu SMP PREEMPT Thu Jan 26 15:18:48 UTC 2012 armv7l Buildd toolchain package versions: launchpad-buildd_110~0.IS.08.04 python-lpbuildd_110~0.IS.08.04 bzr_2.3.4-0ubuntu1. Syncing the system clock with the buildd NTP service... 16 Feb 23:15:08 ntpdate[10788]: adjust time server 10.211.37.1 offset 0.000792 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '1dda6661c646f164ec3f0120d354e8b668e8dc3b', '/home/buildd/filecache-default/bc889b29e9332c7dbba64943354df6525d868b65'] Unpacking chroot for build 1dda6661c646f164ec3f0120d354e8b668e8dc3b RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '1dda6661c646f164ec3f0120d354e8b668e8dc3b'] Mounting chroot for build 1dda6661c646f164ec3f0120d354e8b668e8dc3b RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '1dda6661c646f164ec3f0120d354e8b668e8dc3b', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/glibc/ubuntu precise main', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-updates main restricted universe multiverse'] Overriding sources.list in build-1dda6661c646f164ec3f0120d354e8b668e8dc3b RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '1dda6661c646f164ec3f0120d354e8b668e8dc3b', 'armhf'] Updating debian chroot for build 1dda6661c646f164ec3f0120d354e8b668e8dc3b Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ftpmaster.internal precise-security Release.gpg [198 B] Ign http://ppa.launchpad.net precise InRelease Get:3 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:4 http://ftpmaster.internal precise Release [49.6 kB] Get:5 http://ppa.launchpad.net precise Release.gpg [316 B] Get:6 http://ppa.launchpad.net precise Release [11.9 kB] Get:7 http://ftpmaster.internal precise-security Release [28.9 kB] Get:8 http://ftpmaster.internal precise-updates Release [28.9 kB] Ign http://ppa.launchpad.net precise Release Get:9 http://ftpmaster.internal precise/main armhf Packages [1277 kB] Get:10 http://ppa.launchpad.net precise/main armhf Packages [1490 B] Ign http://ppa.launchpad.net precise/main TranslationIndex Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise/restricted armhf Packages [14 B] Get:12 http://ftpmaster.internal precise/universe armhf Packages [4573 kB] Get:13 http://ftpmaster.internal precise/multiverse armhf Packages [109 kB] Get:14 http://ftpmaster.internal precise/main TranslationIndex [3570 B] Get:15 http://ftpmaster.internal precise/multiverse TranslationIndex [2540 B] Get:16 http://ftpmaster.internal precise/restricted TranslationIndex [2464 B] Get:17 http://ftpmaster.internal precise/universe TranslationIndex [2784 B] Get:18 http://ftpmaster.internal precise-security/main armhf Packages [14 B] Get:19 http://ftpmaster.internal precise-security/restricted armhf Packages [14 B] Get:20 http://ftpmaster.internal precise-security/universe armhf Packages [14 B] Get:21 http://ftpmaster.internal precise-security/multiverse armhf Packages [14 B] Get:22 http://ftpmaster.internal precise-security/main TranslationIndex [70 B] Get:23 http://ftpmaster.internal precise-security/multiverse TranslationIndex [70 B] Get:24 http://ftpmaster.internal precise-security/restricted TranslationIndex [70 B] Get:25 http://ftpmaster.internal precise-security/universe TranslationIndex [70 B] Get:26 http://ftpmaster.internal precise-updates/main armhf Packages [14 B] Get:27 http://ftpmaster.internal precise-updates/restricted armhf Packages [14 B] Get:28 http://ftpmaster.internal precise-updates/universe armhf Packages [14 B] Get:29 http://ftpmaster.internal precise-updates/multiverse armhf Packages [14 B] Get:30 http://ftpmaster.internal precise-updates/main TranslationIndex [70 B] Get:31 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [70 B] Get:32 http://ftpmaster.internal precise-updates/restricted TranslationIndex [70 B] Get:33 http://ftpmaster.internal precise-updates/universe TranslationIndex [70 B] Get:34 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:35 http://ftpmaster.internal precise/multiverse Translation-en [96.5 kB] Get:36 http://ftpmaster.internal precise/restricted Translation-en [2229 B] Get:37 http://ftpmaster.internal precise/universe Translation-en [3353 kB] Get:38 http://ftpmaster.internal precise-security/main Translation-en [14 B] Get:39 http://ftpmaster.internal precise-security/multiverse Translation-en [14 B] Get:40 http://ftpmaster.internal precise-security/restricted Translation-en [14 B] Get:41 http://ftpmaster.internal precise-security/universe Translation-en [14 B] Get:42 http://ftpmaster.internal precise-updates/main Translation-en [14 B] Get:43 http://ftpmaster.internal precise-updates/multiverse Translation-en [14 B] Get:44 http://ftpmaster.internal precise-updates/restricted Translation-en [14 B] Get:45 http://ftpmaster.internal precise-updates/universe Translation-en [14 B] Fetched 10.3 MB in 29s (344 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 1E9377A2BA9EF27F Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https ca-certificates cpp-4.6 debconf debianutils e2fslibs e2fsprogs g++-4.6 gcc-4.6 gcc-4.6-base gzip ifupdown initramfs-tools initramfs-tools-bin insserv libapt-pkg4.12 libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libgcc1 libglib2.0-0 libgomp1 libnih-dbus1 libnih1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng12-0 libsasl2-2 libss2 libssl1.0.0 libstdc++6 libstdc++6-4.6-dev libudev0 linux-libc-dev login mountall multiarch-support openssl passwd pkgbinarymangler udev 46 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 31.7 MB of archives. After this operation, 410 kB disk space will be freed. WARNING: The following packages cannot be authenticated! libnih-dbus1 libc-bin libc6 libnih1 libc6-dev libc-dev-bin linux-libc-dev libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 debianutils e2fslibs e2fsprogs gzip login libapt-pkg4.12 debconf libcomerr2 libpam0g libpam-modules-bin libpam-modules libss2 libssl1.0.0 libglib2.0-0 libpng12-0 libudev0 initramfs-tools initramfs-tools-bin udev mountall libsasl2-2 apt libpam-runtime multiarch-support passwd ifupdown insserv apt-transport-https openssl ca-certificates pkgbinarymangler Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libnih-dbus1 armhf 1.0.3-4ubuntu9 [14.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libc-bin armhf 2.15-0ubuntu2 [1014 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libc6 armhf 2.15-0ubuntu2 [3826 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libnih1 armhf 1.0.3-4ubuntu9 [48.9 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libc6-dev armhf 2.15-0ubuntu2 [2123 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libc-dev-bin armhf 2.15-0ubuntu2 [73.2 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main linux-libc-dev armhf 3.2.0-16.25 [822 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main libgomp1 armhf 4.6.2-14ubuntu2 [23.6 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main gcc-4.6-base armhf 4.6.2-14ubuntu2 [15.8 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main libgcc1 armhf 1:4.6.2-14ubuntu2 [22.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main cpp-4.6 armhf 4.6.2-14ubuntu2 [4100 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main libstdc++6-4.6-dev armhf 4.6.2-14ubuntu2 [1704 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main g++-4.6 armhf 4.6.2-14ubuntu2 [4976 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main gcc-4.6 armhf 4.6.2-14ubuntu2 [4560 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main libstdc++6 armhf 4.6.2-14ubuntu2 [268 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main debianutils armhf 4.2.1ubuntu1 [62.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main e2fslibs armhf 1.42-1ubuntu1 [168 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main e2fsprogs armhf 1.42-1ubuntu1 [949 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main gzip armhf 1.4-1ubuntu2 [85.2 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main login armhf 1:4.1.4.2+svn3283-3ubuntu4 [279 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main libapt-pkg4.12 armhf 0.8.16~exp12ubuntu4 [859 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main debconf all 1.5.41ubuntu2 [142 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main libcomerr2 armhf 1.42-1ubuntu1 [55.7 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main libpam0g armhf 1.1.3-7ubuntu2 [54.5 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main libpam-modules-bin armhf 1.1.3-7ubuntu2 [36.8 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main libpam-modules armhf 1.1.3-7ubuntu2 [242 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libss2 armhf 1.42-1ubuntu1 [59.7 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libssl1.0.0 armhf 1.0.0g-1ubuntu1 [782 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libglib2.0-0 armhf 2.31.16-0ubuntu2 [1016 kB] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libpng12-0 armhf 1.2.46-3ubuntu2 [118 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libudev0 armhf 175-0ubuntu4 [26.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main initramfs-tools all 0.99ubuntu10 [48.7 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main initramfs-tools-bin armhf 0.99ubuntu10 [9720 B] Get:34 http://ftpmaster.internal/ubuntu/ precise/main udev armhf 175-0ubuntu4 [294 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main mountall armhf 2.34 [63.2 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main libsasl2-2 armhf 2.1.25.dfsg1-3 [55.8 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main apt armhf 0.8.16~exp12ubuntu4 [1046 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main libpam-runtime all 1.1.3-7ubuntu2 [40.4 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main multiarch-support armhf 2.15-0ubuntu2 [4484 B] Get:40 http://ftpmaster.internal/ubuntu/ precise/main passwd armhf 1:4.1.4.2+svn3283-3ubuntu4 [804 kB] Get:41 http://ftpmaster.internal/ubuntu/ precise/main ifupdown armhf 0.7~beta2ubuntu6 [44.7 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main insserv armhf 1.14.0-2.1ubuntu1 [47.7 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main apt-transport-https armhf 0.8.16~exp12ubuntu4 [15.2 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main openssl armhf 1.0.0g-1ubuntu1 [508 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main ca-certificates all 20111211 [169 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main pkgbinarymangler all 115 [29.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.7 MB in 8s (3759 kB/s) (Reading database ... 12080 files and directories currently installed.) Preparing to replace libnih-dbus1 1.0.3-4ubuntu5 (using .../libnih-dbus1_1.0.3-4ubuntu9_armhf.deb) ... Unpacking replacement libnih-dbus1 ... Preparing to replace libc-bin 2.13-24ubuntu4 (using .../libc-bin_2.15-0ubuntu2_armhf.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.15-0ubuntu2) ... (Reading database ... 12081 files and directories currently installed.) Preparing to replace libc6 2.13-24ubuntu4 (using .../libc6_2.15-0ubuntu2_armhf.deb) ... Checking for services that may need to be restarted... Checking init scripts... Unpacking replacement libc6 ... Setting up libc6 (2.15-0ubuntu2) ... 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 ... 12086 files and directories currently installed.) Preparing to replace libnih1 1.0.3-4ubuntu5 (using .../libnih1_1.0.3-4ubuntu9_armhf.deb) ... Unpacking replacement libnih1 ... Preparing to replace libc6-dev 2.13-24ubuntu4 (using .../libc6-dev_2.15-0ubuntu2_armhf.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-24ubuntu4 (using .../libc-dev-bin_2.15-0ubuntu2_armhf.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace linux-libc-dev 3.2.0-12.21 (using .../linux-libc-dev_3.2.0-16.25_armhf.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace libgomp1 4.6.2-12ubuntu1 (using .../libgomp1_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.2-12ubuntu1 (using .../gcc-4.6-base_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.2-14ubuntu2) ... (Reading database ... 12091 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.2-12ubuntu1 (using .../libgcc1_1%3a4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.2-14ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12091 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.2-12ubuntu1 (using .../cpp-4.6_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libstdc++6-4.6-dev 4.6.2-12ubuntu1 (using .../libstdc++6-4.6-dev_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.2-12ubuntu1 (using .../g++-4.6_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.2-12ubuntu1 (using .../gcc-4.6_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.2-12ubuntu1 (using .../libstdc++6_4.6.2-14ubuntu2_armhf.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.2-14ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12093 files and directories currently installed.) Preparing to replace debianutils 4.1ubuntu1 (using .../debianutils_4.2.1ubuntu1_armhf.deb) ... Unpacking replacement debianutils ... Setting up debianutils (4.2.1ubuntu1) ... (Reading database ... 12093 files and directories currently installed.) Preparing to replace e2fslibs 1.42~WIP-2011-10-16-1ubuntu1 (using .../e2fslibs_1.42-1ubuntu1_armhf.deb) ... Unpacking replacement e2fslibs ... Setting up e2fslibs (1.42-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12093 files and directories currently installed.) Preparing to replace e2fsprogs 1.42~WIP-2011-10-16-1ubuntu1 (using .../e2fsprogs_1.42-1ubuntu1_armhf.deb) ... Unpacking replacement e2fsprogs ... Setting up e2fsprogs (1.42-1ubuntu1) ... (Reading database ... 12093 files and directories currently installed.) Preparing to replace gzip 1.4-1ubuntu1 (using .../gzip_1.4-1ubuntu2_armhf.deb) ... Unpacking replacement gzip ... Setting up gzip (1.4-1ubuntu2) ... (Reading database ... 12092 files and directories currently installed.) Preparing to replace login 1:4.1.4.2+svn3283-3ubuntu3 (using .../login_1%3a4.1.4.2+svn3283-3ubuntu4_armhf.deb) ... Unpacking replacement login ... Setting up login (1:4.1.4.2+svn3283-3ubuntu4) ... Installing new version of config file /etc/securetty ... (Reading database ... 12092 files and directories currently installed.) Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu3 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu4_armhf.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12092 files and directories currently installed.) Preparing to replace debconf 1.5.41ubuntu1 (using .../debconf_1.5.41ubuntu2_all.deb) ... Unpacking replacement debconf ... Setting up debconf (1.5.41ubuntu2) ... (Reading database ... 12092 files and directories currently installed.) Preparing to replace libcomerr2 1.42~WIP-2011-10-16-1ubuntu1 (using .../libcomerr2_1.42-1ubuntu1_armhf.deb) ... Unpacking replacement libcomerr2 ... Setting up libcomerr2 (1.42-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12092 files and directories currently installed.) Preparing to replace libpam0g 1.1.3-7ubuntu1 (using .../libpam0g_1.1.3-7ubuntu2_armhf.deb) ... Unpacking replacement libpam0g ... Setting up libpam0g (1.1.3-7ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12092 files and directories currently installed.) Preparing to replace libpam-modules-bin 1.1.3-7ubuntu1 (using .../libpam-modules-bin_1.1.3-7ubuntu2_armhf.deb) ... Unpacking replacement libpam-modules-bin ... Setting up libpam-modules-bin (1.1.3-7ubuntu2) ... (Reading database ... 12092 files and directories currently installed.) Preparing to replace libpam-modules 1.1.3-7ubuntu1 (using .../libpam-modules_1.1.3-7ubuntu2_armhf.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.1.3-7ubuntu2) ... (Reading database ... 12092 files and directories currently installed.) Preparing to replace libss2 1.42~WIP-2011-10-16-1ubuntu1 (using .../libss2_1.42-1ubuntu1_armhf.deb) ... Unpacking replacement libss2 ... Setting up libss2 (1.42-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12092 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.0e-3ubuntu1 (using .../libssl1.0.0_1.0.0g-1ubuntu1_armhf.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.0g-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12092 files and directories currently installed.) Preparing to replace libglib2.0-0 2.31.14-0ubuntu1 (using .../libglib2.0-0_2.31.16-0ubuntu2_armhf.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libpng12-0 1.2.46-3ubuntu1 (using .../libpng12-0_1.2.46-3ubuntu2_armhf.deb) ... Unpacking replacement libpng12-0 ... Preparing to replace libudev0 175-0ubuntu3 (using .../libudev0_175-0ubuntu4_armhf.deb) ... Unpacking replacement libudev0 ... Preparing to replace initramfs-tools 0.99ubuntu9 (using .../initramfs-tools_0.99ubuntu10_all.deb) ... Unpacking replacement initramfs-tools ... Preparing to replace initramfs-tools-bin 0.99ubuntu9 (using .../initramfs-tools-bin_0.99ubuntu10_armhf.deb) ... Unpacking replacement initramfs-tools-bin ... Preparing to replace udev 175-0ubuntu3 (using .../udev_175-0ubuntu4_armhf.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace mountall 2.33 (using .../mountall_2.34_armhf.deb) ... Unpacking replacement mountall ... Preparing to replace libsasl2-2 2.1.24~rc1.dfsg1+cvs2011-05-23-4ubuntu3 (using .../libsasl2-2_2.1.25.dfsg1-3_armhf.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace apt 0.8.16~exp12ubuntu3 (using .../apt_0.8.16~exp12ubuntu4_armhf.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu4) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: Total number processed: 2 gpg: unchanged: 2 (Reading database ... 12093 files and directories currently installed.) Preparing to replace libpam-runtime 1.1.3-7ubuntu1 (using .../libpam-runtime_1.1.3-7ubuntu2_all.deb) ... Unpacking replacement libpam-runtime ... Setting up libpam-runtime (1.1.3-7ubuntu2) ... (Reading database ... 12093 files and directories currently installed.) Preparing to replace multiarch-support 2.13-24ubuntu4 (using .../multiarch-support_2.15-0ubuntu2_armhf.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.15-0ubuntu2) ... (Reading database ... 12093 files and directories currently installed.) Preparing to replace passwd 1:4.1.4.2+svn3283-3ubuntu3 (using .../passwd_1%3a4.1.4.2+svn3283-3ubuntu4_armhf.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.4.2+svn3283-3ubuntu4) ... (Reading database ... 12093 files and directories currently installed.) Preparing to replace ifupdown 0.7~beta2ubuntu3 (using .../ifupdown_0.7~beta2ubuntu6_armhf.deb) ... Unpacking replacement ifupdown ... Preparing to replace insserv 1.14.0-2.1 (using .../insserv_1.14.0-2.1ubuntu1_armhf.deb) ... Unpacking replacement insserv ... Preparing to replace apt-transport-https 0.8.16~exp12ubuntu3 (using .../apt-transport-https_0.8.16~exp12ubuntu4_armhf.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace openssl 1.0.0e-3ubuntu1 (using .../openssl_1.0.0g-1ubuntu1_armhf.deb) ... Unpacking replacement openssl ... Preparing to replace ca-certificates 20110502+nmu1ubuntu5 (using .../ca-certificates_20111211_all.deb) ... Unpacking replacement ca-certificates ... Preparing to replace pkgbinarymangler 114 (using .../pkgbinarymangler_115_all.deb) ... Unpacking replacement pkgbinarymangler ... Setting up libnih1 (1.0.3-4ubuntu9) ... Setting up libnih-dbus1 (1.0.3-4ubuntu9) ... Setting up libc-dev-bin (2.15-0ubuntu2) ... Setting up linux-libc-dev (3.2.0-16.25) ... Setting up libc6-dev (2.15-0ubuntu2) ... Setting up libgomp1 (4.6.2-14ubuntu2) ... Setting up cpp-4.6 (4.6.2-14ubuntu2) ... Setting up gcc-4.6 (4.6.2-14ubuntu2) ... Setting up libglib2.0-0 (2.31.16-0ubuntu2) ... No schema files found: doing nothing. Setting up libpng12-0 (1.2.46-3ubuntu2) ... Setting up libudev0 (175-0ubuntu4) ... Setting up initramfs-tools-bin (0.99ubuntu10) ... Setting up libsasl2-2 (2.1.25.dfsg1-3) ... Setting up ifupdown (0.7~beta2ubuntu6) ... Setting up insserv (1.14.0-2.1ubuntu1) ... Setting up apt-transport-https (0.8.16~exp12ubuntu4) ... Setting up openssl (1.0.0g-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up ca-certificates (20111211) ... Clearing symlinks in /etc/ssl/certs...done. Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Setting up pkgbinarymangler (115) ... Setting up udev (175-0ubuntu4) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up mountall (2.34) ... Installing new version of config file /etc/init/mounted-debugfs.conf ... Setting up g++-4.6 (4.6.2-14ubuntu2) ... Setting up initramfs-tools (0.99ubuntu10) ... update-initramfs: deferring update (trigger activated) Setting up libstdc++6-4.6-dev (4.6.2-14ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '1dda6661c646f164ec3f0120d354e8b668e8dc3b', 'armhf', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=COPY', '--architecture=armhf', '--comp=universe', 'samtools_0.1.18-1ubuntu2.dsc'] Initiating build 1dda6661c646f164ec3f0120d354e8b668e8dc3b with 2 processor cores. Automatic build of samtools_0.1.18-1ubuntu2 on musimon by sbuild/armhf 1.170.5 Build started at 20120216-2318 ****************************************************************************** samtools_0.1.18-1ubuntu2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev Checking for already installed source dependencies... debhelper: missing cdbs: missing quilt: missing libncurses5-dev: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper cdbs quilt libncurses5-dev zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autoconf automake autotools-dev bsdmainutils dh-translations diffstat file gettext gettext-base groff-base html2text intltool intltool-debian 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 libtinfo-dev 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 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 ncurses-doc 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 libio-socket-inet6-perl libhtml-form-perl libhtml-format-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-translations diffstat file gettext gettext-base groff-base html2text intltool intltool-debian 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 libncurses5-dev libnet-http-perl libnet-ssleay-perl libpipeline1 libtinfo-dev 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, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 11.7 MB of archives. After this operation, 35.9 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 libmagic1 file mime-support netbase python2.7 python bsdmainutils gettext-base groff-base man-db m4 autoconf autotools-dev automake html2text gettext intltool-debian po-debconf 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-http-perl libnet-ssleay-perl libio-socket-ssl-perl liblwp-protocol-https-perl libwww-robotrules-perl libwww-perl libxml-parser-perl intltool dh-translations python-scour cdbs diffstat libtinfo-dev libncurses5-dev quilt zlib1g-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libexpat1 armhf 2.0.1-7.2 [102 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 armhf 1.2.0-5 [20.7 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libxml2 armhf 2.7.8.dfsg-5.1ubuntu3 [548 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 armhf 0.6.4-2 [82.0 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 armhf 0.9.3-5 [393 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 armhf 0.18.1.1-5ubuntu3 [99.4 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 armhf 5.09-2 [213 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main file armhf 5.09-2 [19.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main netbase all 4.47ubuntu1 [15.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main python2.7 armhf 2.7.2-13ubuntu4 [2580 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main python all 2.7.2-9ubuntu2 [168 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils armhf 8.2.3 [193 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main gettext-base armhf 0.18.1.1-5ubuntu3 [54.7 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main groff-base armhf 1.21-6 [926 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main man-db armhf 2.6.1-1 [699 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise/main m4 armhf 1.4.16-2ubuntu1 [182 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise/main autoconf all 2.68-1ubuntu2 [560 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main autotools-dev all 20120210.1 [42.3 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main automake all 1:1.11.3-1 [571 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise/main html2text armhf 1.3.2a-15 [85.8 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise/main gettext armhf 0.18.1.1-5ubuntu3 [1050 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu2 [618 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise/main liburi-perl all 1.59-1 [90.3 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise/main libencode-locale-perl all 1.02-2 [12.0 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise/main libhttp-date-perl all 6.00-1 [10.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise/main libfile-listing-perl all 6.03-1 [9690 B] Get:30 http://ftpmaster.internal/ubuntu/ precise/main libhtml-tagset-perl all 3.20-2 [13.5 kB] Get:31 http://ftpmaster.internal/ubuntu/ precise/main libhtml-parser-perl armhf 3.69-1build1 [95.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ precise/main libhtml-tree-perl all 4.2-1 [205 kB] Get:33 http://ftpmaster.internal/ubuntu/ precise/main liblwp-mediatypes-perl all 6.01-1 [17.5 kB] Get:34 http://ftpmaster.internal/ubuntu/ precise/main libhttp-message-perl all 6.01-1 [77.6 kB] Get:35 http://ftpmaster.internal/ubuntu/ precise/main libhttp-cookies-perl all 6.00-2 [23.3 kB] Get:36 http://ftpmaster.internal/ubuntu/ precise/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] Get:37 http://ftpmaster.internal/ubuntu/ precise/main libnet-http-perl all 6.02-1 [23.5 kB] Get:38 http://ftpmaster.internal/ubuntu/ precise/main libnet-ssleay-perl armhf 1.42-1build1 [174 kB] Get:39 http://ftpmaster.internal/ubuntu/ precise/main libio-socket-ssl-perl all 1.53-1 [47.5 kB] Get:40 http://ftpmaster.internal/ubuntu/ precise/main liblwp-protocol-https-perl all 6.02-1 [6746 B] Get:41 http://ftpmaster.internal/ubuntu/ precise/main libwww-robotrules-perl all 6.01-1 [14.1 kB] Get:42 http://ftpmaster.internal/ubuntu/ precise/main libwww-perl all 6.03-1 [156 kB] Get:43 http://ftpmaster.internal/ubuntu/ precise/main libxml-parser-perl armhf 2.41-1build1 [302 kB] Get:44 http://ftpmaster.internal/ubuntu/ precise/main intltool all 0.50.1-1 [51.3 kB] Get:45 http://ftpmaster.internal/ubuntu/ precise/main dh-translations all 115 [21.6 kB] Get:46 http://ftpmaster.internal/ubuntu/ precise/main python-scour all 0.26-3 [46.5 kB] Get:47 http://ftpmaster.internal/ubuntu/ precise/main cdbs all 0.4.100ubuntu2 [47.6 kB] Get:48 http://ftpmaster.internal/ubuntu/ precise/main diffstat armhf 1.54-1 [20.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ precise/main libtinfo-dev armhf 5.9-4 [84.0 kB] Get:50 http://ftpmaster.internal/ubuntu/ precise/main libncurses5-dev armhf 5.9-4 [192 kB] Get:51 http://ftpmaster.internal/ubuntu/ precise/main quilt all 0.50-2 [287 kB] Get:52 http://ftpmaster.internal/ubuntu/ precise/main zlib1g-dev armhf 1:1.2.3.4.dfsg-3ubuntu4 [158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.7 MB in 2s (3923 kB/s) Selecting previously unselected package libexpat1. (Reading database ... 12087 files and directories currently installed.) Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_armhf.deb) ... Selecting previously unselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armhf.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu3_armhf.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.4-2_armhf.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_armhf.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_armhf.deb) ... 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Unpacking debhelper (from .../debhelper_9.20120115ubuntu2_all.deb) ... Selecting previously unselected package liburi-perl. Unpacking liburi-perl (from .../liburi-perl_1.59-1_all.deb) ... Selecting previously unselected package libencode-locale-perl. Unpacking libencode-locale-perl (from .../libencode-locale-perl_1.02-2_all.deb) ... Selecting previously unselected package libhttp-date-perl. Unpacking libhttp-date-perl (from .../libhttp-date-perl_6.00-1_all.deb) ... Selecting previously unselected package libfile-listing-perl. Unpacking libfile-listing-perl (from .../libfile-listing-perl_6.03-1_all.deb) ... Selecting previously unselected package libhtml-tagset-perl. Unpacking libhtml-tagset-perl (from .../libhtml-tagset-perl_3.20-2_all.deb) ... Selecting previously unselected package libhtml-parser-perl. Unpacking libhtml-parser-perl (from .../libhtml-parser-perl_3.69-1build1_armhf.deb) ... Selecting previously unselected package libhtml-tree-perl. 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Selecting previously unselected package libio-socket-ssl-perl. Unpacking libio-socket-ssl-perl (from .../libio-socket-ssl-perl_1.53-1_all.deb) ... Selecting previously unselected package liblwp-protocol-https-perl. Unpacking liblwp-protocol-https-perl (from .../liblwp-protocol-https-perl_6.02-1_all.deb) ... Selecting previously unselected package libwww-robotrules-perl. Unpacking libwww-robotrules-perl (from .../libwww-robotrules-perl_6.01-1_all.deb) ... Selecting previously unselected package libwww-perl. Unpacking libwww-perl (from .../libwww-perl_6.03-1_all.deb) ... Selecting previously unselected package libxml-parser-perl. Unpacking libxml-parser-perl (from .../libxml-parser-perl_2.41-1build1_armhf.deb) ... Selecting previously unselected package intltool. Unpacking intltool (from .../intltool_0.50.1-1_all.deb) ... Selecting previously unselected package dh-translations. Unpacking dh-translations (from .../dh-translations_115_all.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_0.4.100ubuntu2_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.54-1_armhf.deb) ... Selecting previously unselected package libtinfo-dev. Unpacking libtinfo-dev (from .../libtinfo-dev_5.9-4_armhf.deb) ... Selecting previously unselected package libncurses5-dev. Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-4_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ... Selecting previously unselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu4_armhf.deb) ... Setting up libexpat1 (2.0.1-7.2) ... Setting up libpipeline1 (1.2.0-5) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu3) ... Setting up libcroco3 (0.6.4-2) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up mime-support (3.51-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up netbase (4.47ubuntu1) ... Setting up python2.7 (2.7.2-13ubuntu4) ... Setting up python (2.7.2-9ubuntu2) ... Setting up bsdmainutils (8.2.3) ... 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 (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-6) ... Setting up man-db (2.6.1-1) ... Building database of manual pages ... Setting up m4 (1.4.16-2ubuntu1) ... Setting up autoconf (2.68-1ubuntu2) ... Setting up autotools-dev (20120210.1) ... Setting up automake (1:1.11.3-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up debhelper (9.20120115ubuntu2) ... Setting up liburi-perl (1.59-1) ... Setting up libencode-locale-perl (1.02-2) ... Setting up libhttp-date-perl (6.00-1) ... Setting up libfile-listing-perl (6.03-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.69-1build1) ... Setting up libhtml-tree-perl (4.2-1) ... Setting up liblwp-mediatypes-perl (6.01-1) ... Setting up libhttp-message-perl (6.01-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-http-perl (6.02-1) ... Setting up libnet-ssleay-perl (1.42-1build1) ... Setting up libio-socket-ssl-perl (1.53-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up python-scour (0.26-3) ... Setting up diffstat (1.54-1) ... Setting up libtinfo-dev (5.9-4) ... Setting up libncurses5-dev (5.9-4) ... Setting up quilt (0.50-2) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu4) ... Setting up liblwp-protocol-https-perl (6.02-1) ... Setting up libwww-perl (6.03-1) ... Setting up libxml-parser-perl (2.41-1build1) ... Setting up intltool (0.50.1-1) ... Setting up dh-translations (115) ... Setting up cdbs (0.4.100ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu2 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu5 gcc-4.6_4.6.2-14ubuntu2 g++-4.6_4.6.2-14ubuntu2 binutils_2.22-5ubuntu1 libstdc++6-4.6-dev_4.6.2-14ubuntu2 libstdc++6_4.6.2-14ubuntu2 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Sat Dec 3 04:36:45 2011 UTC using DSA key ID C6CEA0C9 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1ubuntu2.dsc dpkg-source: info: extracting samtools in samtools-0.1.18 dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2 dpkg-source: info: unpacking samtools_0.1.18-1ubuntu2.debian.tar.gz dpkg-source: info: applying no-pileup-tests.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2 dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro dpkg-buildpackage: source package samtools dpkg-buildpackage: source version 0.1.18-1ubuntu2 dpkg-source --before-build samtools-0.1.18 dpkg-buildpackage: host architecture armhf /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 -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" -k clean make[1]: Entering directory `/build/buildd/samtools-0.1.18' make[2]: Entering directory `/build/buildd/samtools-0.1.18' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory `/build/buildd/samtools-0.1.18' make[2]: Entering directory `/build/buildd/samtools-0.1.18/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory `/build/buildd/samtools-0.1.18/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.18/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a make[2]: Leaving directory `/build/buildd/samtools-0.1.18/misc' make[1]: Leaving directory `/build/buildd/samtools-0.1.18' rm -f debian/stamp-makefile-check dh_clean /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/samtools-0.1.18' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.18' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/build/buildd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch no-pileup-tests.patch Restoring examples/Makefile No patches applied rm -rf ./.pc rm -f debian/stamp-patch* rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf 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/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/samtools-0.1.18' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.18' cd . && QUILT_PATCHES=/build/buildd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch no-pileup-tests.patch patching file examples/Makefile Now at patch no-pileup-tests.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/build/buildd/samtools-0.1.18' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/build/buildd/samtools-0.1.18' /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" all all-recur razip lib make[1]: Entering directory `/build/buildd/samtools-0.1.18' make[2]: Entering directory `/build/buildd/samtools-0.1.18' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o bgzf.c: In function 'bgzf_close': bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o bam_import.c: In function 'append_text': bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function 'bam_index_load_core': bam_index.c:330:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:337:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:350:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:353:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:357:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:361:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:371:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bam_index.c:375:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function 'razf_close': razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c: In function 'razf_end_flush': razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c: In function '_razf_write': razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c: In function 'save_zindex': razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c: In function 'razf_flush': razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o knetfile.c: In function 'khttp_connect_file': knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] knetfile.c: In function 'kftp_send_cmd': knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function 'bam_reheader': bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function 'kpa_glocal': kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[2]: Leaving directory `/build/buildd/samtools-0.1.18' make[2]: Entering directory `/build/buildd/samtools-0.1.18/bcftools' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function 'bcf_em1': em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[2]: Leaving directory `/build/buildd/samtools-0.1.18/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.18/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/build/buildd/samtools-0.1.18/misc' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o cut_target.c: In function 'main_cut_target': cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz make[2]: Entering directory `/build/buildd/samtools-0.1.18' make[3]: Entering directory `/build/buildd/samtools-0.1.18' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.18' make[3]: Entering directory `/build/buildd/samtools-0.1.18/bcftools' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.18/bcftools' make[3]: Entering directory `/build/buildd/samtools-0.1.18/misc' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/build/buildd/samtools-0.1.18/misc' gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz make[2]: Leaving directory `/build/buildd/samtools-0.1.18' make[2]: Entering directory `/build/buildd/samtools-0.1.18/bcftools' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz make[2]: Leaving directory `/build/buildd/samtools-0.1.18/bcftools' make[2]: Entering directory `/build/buildd/samtools-0.1.18/misc' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c seqtk.c: In function 'stk_comp': seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable] seqtk.c: In function 'stk_subseq': seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] seqtk.c: In function 'stk_mergefa': seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] seqtk.c: In function 'stk_famask': seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat] seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat] gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz make[2]: Leaving directory `/build/buildd/samtools-0.1.18/misc' gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o razip.c: In function 'main': razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] razip.c: In function 'write_open': razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/build/buildd/samtools-0.1.18' touch debian/stamp-makefile-build /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" -C examples all make[1]: Entering directory `/build/buildd/samtools-0.1.18/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[1]: Leaving directory `/build/buildd/samtools-0.1.18/examples' touch debian/stamp-makefile-check /usr/bin/fakeroot debian/rules binary-arch test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target Adding cdbs dependencies to debian/samtools.substvars dh_installdirs -psamtools Adding cdbs dependencies to debian/libbam-dev.substvars dh_installdirs -plibbam-dev dh_installdocs -psamtools ./NEWS ./AUTHORS dh_installexamples -psamtools dh_installman -psamtools dh_installinfo -psamtools dh_installmenu -psamtools dh_installcron -psamtools dh_installinit -psamtools dh_installdebconf -psamtools dh_installemacsen -psamtools dh_installcatalogs -psamtools dh_installpam -psamtools dh_installlogrotate -psamtools dh_installlogcheck -psamtools dh_installchangelogs -psamtools ./ChangeLog dh_installudev -psamtools dh_lintian -psamtools dh_bugfiles -psamtools dh_install -psamtools dh_link -psamtools dh_installmime -psamtools dh_installgsettings -psamtools install -m 644 bcftools/README /build/buildd/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools ln -s samtools.1.gz /build/buildd/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz dh_installdocs -plibbam-dev ./NEWS ./AUTHORS dh_installexamples -plibbam-dev dh_installman -plibbam-dev dh_installinfo -plibbam-dev dh_installmenu -plibbam-dev dh_installcron -plibbam-dev dh_installinit -plibbam-dev dh_installdebconf -plibbam-dev dh_installemacsen -plibbam-dev dh_installcatalogs -plibbam-dev dh_installpam -plibbam-dev dh_installlogrotate -plibbam-dev dh_installlogcheck -plibbam-dev dh_installchangelogs -plibbam-dev ./ChangeLog dh_installudev -plibbam-dev dh_lintian -plibbam-dev dh_bugfiles -plibbam-dev dh_install -plibbam-dev dh_link -plibbam-dev dh_installmime -plibbam-dev dh_installgsettings -plibbam-dev dh_strip -psamtools dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: samtools libbam-dev dh_strip debug symbol extraction: packages to act on: samtools dh_strip debug symbol extraction: ignored packages: dpkg-deb: warning: '/build/buildd/samtools-0.1.18/debian/samtools-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `samtools-dbgsym' in `../samtools-dbgsym_0.1.18-1ubuntu2_armhf.ddeb'. dh_compress -psamtools dh_fixperms -psamtools dh_makeshlibs -psamtools sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py dh_strip -plibbam-dev dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: samtools libbam-dev dh_strip debug symbol extraction: packages to act on: libbam-dev dh_strip debug symbol extraction: ignored packages: libbam-dev is already stripped, ignoring dh_compress -plibbam-dev dh_fixperms -plibbam-dev dh_makeshlibs -plibbam-dev dh_installdeb -psamtools dh_perl -psamtools dh_shlibdeps -psamtools dh_installdeb -plibbam-dev dh_perl -plibbam-dev dh_shlibdeps -plibbam-dev dh_gencontrol -psamtools dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends} # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -psamtools ; fi dh_md5sums -psamtools dh_builddeb -psamtools -- -Z=xz INFO: pkgstriptranslations version 115 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package samtools took 0 s dpkg-deb: warning: 'debian/samtools/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `samtools' in `../samtools_0.1.18-1ubuntu2_armhf.deb'. dh_gencontrol -plibbam-dev dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends} # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -plibbam-dev ; fi dh_md5sums -plibbam-dev dh_builddeb -plibbam-dev -- -Z=xz INFO: pkgstriptranslations version 115 pkgstriptranslations: processing libbam-dev (in debian/libbam-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libbam-dev/DEBIAN/control, package libbam-dev, directory debian/libbam-dev .. removing usr/share/doc/libbam-dev/changelog.gz pkgstripfiles: Truncating usr/share/doc/libbam-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package libbam-dev took 0 s dpkg-deb: warning: 'debian/libbam-dev/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1ubuntu2_armhf.deb'. dpkg-genchanges -B -mUbuntu/armel Build Daemon >../samtools_0.1.18-1ubuntu2_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build samtools-0.1.18 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120216-2322 Publishing debug debs. chroot-autobuild/build/buildd/samtools_0.1.18-1ubuntu2_armhf.deb: new debian package, version 2.0. size 472386 bytes: control archive= 1821 bytes. 935 bytes, 18 lines control 2383 bytes, 36 lines md5sums Package: samtools Version: 0.1.18-1ubuntu2 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 836 Pre-Depends: dpkg (>= 1.15.6) Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.4.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3.dfsg) Suggests: python Section: science Priority: optional Homepage: http://samtools.sourceforge.net Description: processing sequence alignments in SAM and BAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP server. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/libbam-dev_0.1.18-1ubuntu2_armhf.deb: new debian package, version 2.0. size 109012 bytes: control archive= 975 bytes. 790 bytes, 17 lines control 643 bytes, 10 lines md5sums Package: libbam-dev Source: samtools Version: 0.1.18-1ubuntu2 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 329 Pre-Depends: dpkg (>= 1.15.6) Section: libdevel Priority: optional Homepage: http://samtools.sourceforge.net Description: manipulates nucleotide sequence alignments in BAM or SAM format The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/samtools_0.1.18-1ubuntu2_armhf.deb: drwxr-xr-x root/root 0 2012-02-16 23:22 ./ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/lib/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/lib/samtools/ -rwxr-xr-x root/root 9724 2012-02-16 23:22 ./usr/lib/samtools/md5sum-lite -rwxr-xr-x root/root 9748 2012-02-16 23:22 ./usr/lib/samtools/md5fa -rwxr-xr-x root/root 13924 2012-02-16 23:22 ./usr/lib/samtools/wgsim -rwxr-xr-x root/root 9760 2012-02-16 23:22 ./usr/lib/samtools/maq2sam-long -rwxr-xr-x root/root 9760 2012-02-16 23:22 ./usr/lib/samtools/maq2sam-short drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/man/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/man/man1/ -rw-r--r-- root/root 430 2012-02-16 23:22 ./usr/share/man/man1/razip.1.gz -rw-r--r-- root/root 9890 2012-02-16 23:22 ./usr/share/man/man1/samtools.1.gz drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/doc/samtools/ -rw-r--r-- root/root 1200 2012-02-16 23:22 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference -rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/doc/samtools/examples/ -rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam -rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt -rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 126609 2012-02-16 23:22 ./usr/share/doc/samtools/examples/ex1.bam.gz -rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 1966 2012-02-16 23:22 ./usr/share/doc/samtools/README.bcftools -rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz -rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/samtools/ -rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl -rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl -rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl -rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl -rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl -rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl -rwxr-xr-x root/root 5778 2012-02-16 23:22 ./usr/share/samtools/varfilter.py -rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl -rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl -rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl -rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl -rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl -rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/bin/ -rwxr-xr-x root/root 242964 2012-02-16 23:22 ./usr/bin/samtools -rwxr-xr-x root/root 18100 2012-02-16 23:22 ./usr/bin/razip -rwxr-xr-x root/root 88148 2012-02-16 23:22 ./usr/bin/bcftools lrwxrwxrwx root/root 0 2012-02-16 23:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz chroot-autobuild/build/buildd/libbam-dev_0.1.18-1ubuntu2_armhf.deb: drwxr-xr-x root/root 0 2012-02-16 23:22 ./ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/lib/ -rw-r--r-- root/root 195018 2012-02-16 23:22 ./usr/lib/libbam.a drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/include/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/include/samtools/ -rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h -rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h -rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h -rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h -rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-02-16 23:22 ./usr/share/doc/libbam-dev/ -rw-r--r-- root/root 1206 2012-02-16 23:22 ./usr/share/doc/libbam-dev/changelog.Debian.gz -rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS -rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz -rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright samtools_0.1.18-1ubuntu2_armhf.changes: Format: 1.8 Date: Fri, 02 Dec 2011 21:19:17 -0700 Source: samtools Binary: samtools libbam-dev Architecture: armhf Version: 0.1.18-1ubuntu2 Distribution: precise Urgency: low Maintainer: Ubuntu/armel Build Daemon Changed-By: Adam Conrad Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format samtools - processing sequence alignments in SAM and BAM formats Changes: samtools (0.1.18-1ubuntu2) precise; urgency=low . * No-change rebuild to drop spurious libsfgcc1 dependency on armhf. Checksums-Sha1: 8bbb4da5813e9aefba787ce3797e56e7a17c370b 472386 samtools_0.1.18-1ubuntu2_armhf.deb 7e166cf57d2add0831497ff3614d62d14d849af7 109012 libbam-dev_0.1.18-1ubuntu2_armhf.deb Checksums-Sha256: def82a4f6f7053538decdc8f90db9edc0a2e5101a4bc1b2c46c8d6622cb33523 472386 samtools_0.1.18-1ubuntu2_armhf.deb 1d1cffe87e909a13c087c1e13a62e48ed40ba11f0e1ab8adcd203eb8ff1dd828 109012 libbam-dev_0.1.18-1ubuntu2_armhf.deb Files: 88eb6c530543a767ea9e88daa1feef3e 472386 science optional samtools_0.1.18-1ubuntu2_armhf.deb 7f27cc7084a032a67d9436c053f07df3 109012 libdevel optional libbam-dev_0.1.18-1ubuntu2_armhf.deb Original-Maintainer: Debian Med Packaging Team ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/samtools-0.1.18 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base libhttp-message-perl mime-support m4 gettext file zlib1g-dev libhtml-parser-perl intltool libhttp-cookies-perl libwww-perl liburi-perl libhtml-tree-perl autotools-dev po-debconf libnet-http-perl quilt dh-translations libxml-parser-perl libcroco3 libhtml-tagset-perl libxml2 netbase libgettextpo0 automake python-scour libhttp-date-perl man-db libnet-ssleay-perl libfile-listing-perl libencode-locale-perl intltool-debian libhttp-negotiate-perl python2.7 libio-socket-ssl-perl liblwp-protocol-https-perl cdbs diffstat html2text libwww-robotrules-perl gettext-base debhelper libunistring0 python libncurses5-dev libtinfo-dev libmagic1 libpipeline1 libexpat1 bsdmainutils liblwp-mediatypes-perl autoconf (Reading database ... 14959 files and directories currently installed.) Removing zlib1g-dev ... Removing quilt ... Purging configuration files for quilt ... Removing cdbs ... Removing diffstat ... Removing libncurses5-dev ... Removing libtinfo-dev ... Removing dh-translations ... Removing python-scour ... Removing debhelper ... Removing python ... Purging configuration files for python ... Removing intltool ... Removing po-debconf ... Removing libxml-parser-perl ... Removing automake ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing html2text ... Purging configuration files for html2text ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing autoconf ... Purging configuration files for autoconf ... Removing groff-base ... Purging configuration files for groff-base ... Removing mime-support ... Purging configuration files for mime-support ... Removing m4 ... Removing gettext ... Removing file ... Removing autotools-dev ... Removing libgettextpo0 ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing libwww-perl ... Removing libhtml-tree-perl ... Removing libfile-listing-perl ... Removing libhttp-negotiate-perl ... Removing liblwp-protocol-https-perl ... Removing libwww-robotrules-perl ... Removing libhttp-cookies-perl ... Removing libnet-http-perl ... Removing libio-socket-ssl-perl ... Removing libhttp-message-perl ... Removing libhtml-parser-perl ... Removing liburi-perl ... Removing libhtml-tagset-perl ... Removing netbase ... Purging configuration files for netbase ... Removing libhttp-date-perl ... Removing libnet-ssleay-perl ... Removing libencode-locale-perl ... Removing liblwp-mediatypes-perl ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20120216-2323 Build needed 00:03:32, 9444k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '1dda6661c646f164ec3f0120d354e8b668e8dc3b'] Scanning for processes to kill in build /home/buildd/build-1dda6661c646f164ec3f0120d354e8b668e8dc3b/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '1dda6661c646f164ec3f0120d354e8b668e8dc3b'] Unmounting chroot for build 1dda6661c646f164ec3f0120d354e8b668e8dc3b... none /home/buildd/build-1dda6661c646f164ec3f0120d354e8b668e8dc3b/chroot-autobuild/proc proc rw,relatime 0 0 none /home/buildd/build-1dda6661c646f164ec3f0120d354e8b668e8dc3b/chroot-autobuild/dev/pts devpts rw,relatime,mode=600,ptmxmode=000 0 0 none /home/buildd/build-1dda6661c646f164ec3f0120d354e8b668e8dc3b/chroot-autobuild/sys sysfs rw,relatime 0 0 none /home/buildd/build-1dda6661c646f164ec3f0120d354e8b668e8dc3b/chroot-autobuild/dev/shm tmpfs rw,relatime 0 0 RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '1dda6661c646f164ec3f0120d354e8b668e8dc3b'] Removing build 1dda6661c646f164ec3f0120d354e8b668e8dc3b