RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-019 4.3.0-2-generic #11-Ubuntu SMP Fri Dec 4 20:37:49 UTC 2015 s390x Buildd toolchain package versions: launchpad-buildd_136 python-lpbuildd_136 sbuild_0.66.0-5ubuntu1 dpkg-dev_1.18.3ubuntu1 python-debian_0.1.27ubuntu1. Syncing the system clock with the buildd NTP service... 31 Dec 17:07:50 ntpdate[34662]: adjust time server 10.211.37.1 offset -0.000004 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8788404', '/home/buildd/filecache-default/8808aeb45a9438550e8005f67e1dc6d720c06f47'] Unpacking chroot for build PACKAGEBUILD-8788404 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8788404'] Mounting chroot for build PACKAGEBUILD-8788404 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8788404', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8788404 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8788404', 's390x'] Updating debian chroot for build PACKAGEBUILD-8788404 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Ign http://archive-team.internal xenial InRelease Ign http://archive-team.internal xenial Release.gpg Get:2 http://archive-team.internal xenial Release [755 B] Ign http://archive-team.internal xenial/main s390x Packages/DiffIndex Get:3 http://archive-team.internal xenial/main Translation-en [676 kB] Get:4 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:5 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:6 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:7 http://ftpmaster.internal xenial/main s390x Packages [1413 kB] Get:8 http://archive-team.internal xenial/main s390x Packages [1642 kB] Get:9 http://ftpmaster.internal xenial/universe s390x Packages [6558 kB] Get:10 http://ftpmaster.internal xenial/main Translation-en [848 kB] Get:11 http://ftpmaster.internal xenial/universe Translation-en [4760 kB] Get:12 http://ftpmaster.internal xenial-security/main s390x Packages [28 B] Get:13 http://ftpmaster.internal xenial-security/universe s390x Packages [28 B] Get:14 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:15 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/main s390x Packages [28 B] Get:17 http://ftpmaster.internal xenial-updates/universe s390x Packages [28 B] Get:18 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:19 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:20 http://ftpmaster.internal xenial-proposed/main s390x Packages [109 kB] Get:21 http://ftpmaster.internal xenial-proposed/universe s390x Packages [353 kB] Get:22 http://ftpmaster.internal xenial-proposed/main Translation-en [64.1 kB] Get:23 http://ftpmaster.internal xenial-proposed/universe Translation-en [237 kB] Fetched 17.3 MB in 18s (915 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: apt apt-transport-https binutils cpp-5 diffutils dmsetup g++-5 gcc-5 gcc-5-base grep libapparmor1 libapt-pkg4.16 libatomic1 libcc1-0 libdevmapper1.02.1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libkeyutils1 libldap-2.4-2 libmpfr4 libncurses5 libncursesw5 libp11-kit0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libudev1 linux-libc-dev ncurses-base ncurses-bin openssl perl perl-base pkgbinarymangler procps systemd systemd-sysv udev 49 upgraded, 4 newly installed, 1 to remove and 0 not upgraded. Need to get 99.1 MB of archives. After this operation, 29.8 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libapt-pkg4.16 Authentication warning overridden. Get:1 http://archive-team.internal/bootstrap/s390x-stage2/ xenial/main libapt-pkg4.16 s390x 1.0.10.2ubuntu1 [601 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main diffutils s390x 1:3.3-3 [158 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep s390x 2.22-1 [145 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 s390x 6.0+20151024-2ubuntu1 [90.2 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 s390x 6.0+20151024-2ubuntu1 [75.4 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 s390x 6.0+20151024-2ubuntu1 [108 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin s390x 6.0+20151024-2ubuntu1 [134 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-modules-5.22 all 5.22.1-3 [2648 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libperl5.22 s390x 5.22.1-3 [3220 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl s390x 5.22.1-3 [237 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-base s390x 5.22.1-3 [1245 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 s390x 5.3.1-4ubuntu1 [38.5 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main binutils s390x 2.25.90.20151211-0ubuntu2 [1057 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base s390x 5.3.1-4ubuntu1 [16.3 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 s390x 1:5.3.1-4ubuntu1 [24.8 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 s390x 5.3.1-4ubuntu1 [53.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 s390x 5.3.1-4ubuntu1 [7966 B] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 s390x 5.3.1-4ubuntu1 [27.1 MB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev s390x 5.3.1-4ubuntu1 [1376 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev s390x 5.3.1-4ubuntu1 [218 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 s390x 5.3.1-4ubuntu1 [25.4 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 s390x 5.3.1-4ubuntu1 [25.1 MB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 s390x 5.3.1-4ubuntu1 [398 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 s390x 3.1.3-2 [187 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 s390x 1.1.10 [642 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main apt s390x 1.1.10 [948 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main udev s390x 228-2ubuntu2 [948 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 s390x 228-2ubuntu2 [53.6 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 s390x 2.4-3 [53.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 s390x 2:3.3.10-4ubuntu1 [31.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main procps s390x 2:3.3.10-4ubuntu1 [221 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapparmor1 s390x 2.10-0ubuntu9 [29.0 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 s390x 228-2ubuntu2 [189 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main systemd s390x 228-2ubuntu2 [3160 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv s390x 228-2ubuntu2 [15.1 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libldap-2.4-2 s390x 2.4.41+dfsg-1ubuntu3 [151 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 s390x 2:1.02.110-1ubuntu2 [133 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 s390x 1.21-1 [33.7 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 s390x 1.6.4-4 [297 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:42 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 s390x 2.4-3 [74.3 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 s390x 3.2.1-4 [16.3 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libp11-kit0 s390x 0.23.2-3 [97.5 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 s390x 1.0.2e-1ubuntu1 [794 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 s390x 4.7-3 [41.4 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup s390x 2:1.02.110-1ubuntu2 [57.5 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 s390x 2.2.3-2ubuntu3 [37.7 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https s390x 1.1.10 [24.3 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 s390x 1.5.9-8ubuntu1 [9918 B] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main openssl s390x 1.0.2e-1ubuntu1 [477 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev s390x 4.3.0-5.16 [810 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 99.1 MB in 1min 19s (1249 kB/s) (Reading database ... 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Setting up libtinfo5:s390x (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.0+20151024-2ubuntu1_s390x.deb ... Unpacking libncursesw5:s390x (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncursesw5:s390x (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.0+20151024-2ubuntu1_s390x.deb ... Unpacking ncurses-bin (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-bin (6.0+20151024-2ubuntu1) ... dpkg: perl-modules: dependency problems, but removing anyway as you requested: perl depends on perl-modules (>= 5.20.2-6). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11403 files and directories currently installed.) Removing perl-modules (5.20.2-6) ... Purging configuration files for perl-modules (5.20.2-6) ... (Reading database ... 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Unpacking libperl5.22:s390x (5.22.1-3) ... Preparing to unpack .../perl-base_5.22.1-3_s390x.deb ... Unpacking perl-base (5.22.1-3) over (5.20.2-6) ... Setting up perl-base (5.22.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11979 files and directories currently installed.) Preparing to unpack .../libcc1-0_5.3.1-4ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11979 files and directories currently installed.) Preparing to unpack .../libgomp1_5.3.1-4ubuntu1_s390x.deb ... Unpacking libgomp1:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../libatomic1_5.3.1-4ubuntu1_s390x.deb ... Unpacking libatomic1:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../g++-5_5.3.1-4ubuntu1_s390x.deb ... Unpacking g++-5 (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../libstdc++-5-dev_5.3.1-4ubuntu1_s390x.deb ... Unpacking libstdc++-5-dev:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../libgcc-5-dev_5.3.1-4ubuntu1_s390x.deb ... Unpacking libgcc-5-dev:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../gcc-5_5.3.1-4ubuntu1_s390x.deb ... Unpacking gcc-5 (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../cpp-5_5.3.1-4ubuntu1_s390x.deb ... Unpacking cpp-5 (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Preparing to unpack .../libstdc++6_5.3.1-4ubuntu1_s390x.deb ... Unpacking libstdc++6:s390x (5.3.1-4ubuntu1) over (5.2.1-27ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libstdc++6:s390x (5.3.1-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11978 files and directories currently installed.) Preparing to unpack .../libmpfr4_3.1.3-2_s390x.deb ... Unpacking libmpfr4:s390x (3.1.3-2) over (3.1.3-1) ... Preparing to unpack .../libapt-pkg4.16_1.0.10.2ubuntu1_s390x.deb ... Unpacking libapt-pkg4.16:s390x (1.0.10.2ubuntu1) over (1.0.10.2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapt-pkg4.16:s390x (1.0.10.2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11978 files and directories currently installed.) Preparing to unpack .../archives/apt_1.1.10_s390x.deb ... Unpacking apt (1.1.10) over (1.0.10.2ubuntu1) ... Selecting previously unselected package libapt-pkg5.0:s390x. Preparing to unpack .../libapt-pkg5.0_1.1.10_s390x.deb ... Unpacking libapt-pkg5.0:s390x (1.1.10) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapt-pkg5.0:s390x (1.1.10) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12006 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.0+20151024-2ubuntu1_all.deb ... Unpacking ncurses-base (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-base (6.0+20151024-2ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12007 files and directories currently installed.) Preparing to unpack .../udev_228-2ubuntu2_s390x.deb ... Unpacking udev (228-2ubuntu2) over (228-2ubuntu1) ... Preparing to unpack .../libudev1_228-2ubuntu2_s390x.deb ... Unpacking libudev1:s390x (228-2ubuntu2) over (228-2ubuntu1) ... Processing triggers for systemd (228-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libudev1:s390x (228-2ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12005 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_s390x.deb ... Unpacking libselinux1:s390x (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:s390x (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Selecting previously unselected package libprocps4:s390x. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12005 files and directories currently installed.) Preparing to unpack .../libprocps4_2%3a3.3.10-4ubuntu1_s390x.deb ... Unpacking libprocps4:s390x (2:3.3.10-4ubuntu1) ... Preparing to unpack .../procps_2%3a3.3.10-4ubuntu1_s390x.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.10-4ubuntu1) over (1:3.3.9-1ubuntu8) ... Preparing to unpack .../libapparmor1_2.10-0ubuntu9_s390x.deb ... Unpacking libapparmor1:s390x (2.10-0ubuntu9) over (2.10-0ubuntu8) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapparmor1:s390x (2.10-0ubuntu9) ... Processing triggers for systemd (228-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12014 files and directories currently installed.) Preparing to unpack .../libsystemd0_228-2ubuntu2_s390x.deb ... Unpacking libsystemd0:s390x (228-2ubuntu2) over (228-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsystemd0:s390x (228-2ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12014 files and directories currently installed.) Preparing to unpack .../systemd_228-2ubuntu2_s390x.deb ... Unpacking systemd (228-2ubuntu2) over (228-2ubuntu1) ... Setting up systemd (228-2ubuntu2) ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Operation failed: No such file or directory Removing obsolete conffile /etc/X11/xinit/xinitrc.d/50-systemd-user.sh ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../systemd-sysv_228-2ubuntu2_s390x.deb ... Unpacking systemd-sysv (228-2ubuntu2) over (228-2ubuntu1) ... Setting up systemd-sysv (228-2ubuntu2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libldap-2.4-2_2.4.41+dfsg-1ubuntu3_s390x.deb ... Unpacking libldap-2.4-2:s390x (2.4.41+dfsg-1ubuntu3) over (2.4.41+dfsg-1ubuntu2) ... Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.110-1ubuntu2_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.110-1ubuntu2) over (2:1.02.99-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libdevmapper1.02.1:s390x (2:1.02.110-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.21-1_s390x.deb ... Unpacking libgpg-error0:s390x (1.21-1) over (1.20-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgpg-error0:s390x (1.21-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.4-4_s390x.deb ... Unpacking libgcrypt20:s390x (1.6.4-4) over (1.6.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgcrypt20:s390x (1.6.4-4) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.4-3_all.deb ... Unpacking libsemanage-common (2.4-3) over (2.3-1build2) ... Setting up libsemanage-common (2.4-3) ... Installing new version of config file /etc/selinux/semanage.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.4-3_s390x.deb ... Unpacking libsemanage1:s390x (2.4-3) over (2.3-1build2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsemanage1:s390x (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12016 files and directories currently installed.) Preparing to unpack .../libffi6_3.2.1-4_s390x.deb ... Unpacking libffi6:s390x (3.2.1-4) over (3.2.1-3) ... Preparing to unpack .../libp11-kit0_0.23.2-3_s390x.deb ... Unpacking libp11-kit0:s390x (0.23.2-3) over (0.23.1-3) ... Preparing to unpack .../libssl1.0.0_1.0.2e-1ubuntu1_s390x.deb ... Unpacking libssl1.0.0:s390x (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu2) ... Preparing to unpack .../libtasn1-6_4.7-3_s390x.deb ... Unpacking libtasn1-6:s390x (4.7-3) over (4.7-2) ... Preparing to unpack .../dmsetup_2%3a1.02.110-1ubuntu2_s390x.deb ... Unpacking dmsetup (2:1.02.110-1ubuntu2) over (2:1.02.99-1ubuntu1) ... Preparing to unpack .../libseccomp2_2.2.3-2ubuntu3_s390x.deb ... Unpacking libseccomp2:s390x (2.2.3-2ubuntu3) over (2.2.3-2ubuntu1) ... Preparing to unpack .../apt-transport-https_1.1.10_s390x.deb ... Unpacking apt-transport-https (1.1.10) over (1.0.10.2ubuntu1) ... Preparing to unpack .../libkeyutils1_1.5.9-8ubuntu1_s390x.deb ... Unpacking libkeyutils1:s390x (1.5.9-8ubuntu1) over (1.5.9-5ubuntu1) ... Preparing to unpack .../openssl_1.0.2e-1ubuntu1_s390x.deb ... Unpacking openssl (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_4.3.0-5.16_s390x.deb ... Unpacking linux-libc-dev:s390x (4.3.0-5.16) over (4.3.0-1.10) ... Preparing to unpack .../pkgbinarymangler_125_all.deb ... Unpacking pkgbinarymangler (125) over (123) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:s390x (6.0+20151024-2ubuntu1) ... Setting up perl-modules-5.22 (5.22.1-3) ... Setting up libperl5.22:s390x (5.22.1-3) ... Setting up perl (5.22.1-3) ... Setting up libcc1-0:s390x (5.3.1-4ubuntu1) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgomp1:s390x (5.3.1-4ubuntu1) ... Setting up libatomic1:s390x (5.3.1-4ubuntu1) ... Setting up libmpfr4:s390x (3.1.3-2) ... Setting up cpp-5 (5.3.1-4ubuntu1) ... Setting up libgcc-5-dev:s390x (5.3.1-4ubuntu1) ... Setting up gcc-5 (5.3.1-4ubuntu1) ... Setting up libstdc++-5-dev:s390x (5.3.1-4ubuntu1) ... Setting up g++-5 (5.3.1-4ubuntu1) ... Setting up apt (1.1.10) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libprocps4:s390x (2:3.3.10-4ubuntu1) ... Setting up procps (2:3.3.10-4ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up udev (228-2ubuntu2) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up libldap-2.4-2:s390x (2.4.41+dfsg-1ubuntu3) ... Setting up libffi6:s390x (3.2.1-4) ... Setting up libp11-kit0:s390x (0.23.2-3) ... Setting up libssl1.0.0:s390x (1.0.2e-1ubuntu1) ... Setting up libtasn1-6:s390x (4.7-3) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libseccomp2:s390x (2.2.3-2ubuntu3) ... Setting up apt-transport-https (1.1.10) ... Setting up libkeyutils1:s390x (1.5.9-8ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up linux-libc-dev:s390x (4.3.0-5.16) ... Setting up pkgbinarymangler (125) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8788404', 's390x', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=xenial-proposed', '--purge=never', '--nolog', 'rna-star_2.5.0a+dfsg-1.dsc'] Initiating build PACKAGEBUILD-8788404 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.3.0-2-generic #11-Ubuntu SMP Fri Dec 4 20:37:49 UTC 2015 s390x sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on z13-019.buildd +==============================================================================+ | rna-star 2.5.0a+dfsg-1 (s390x) 31 Dec 2015 17:09 | +==============================================================================+ Package: rna-star Version: 2.5.0a+dfsg-1 Source Version: 2.5.0a+dfsg-1 Distribution: xenial-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/rna-star-Gnt4Ck/rna-star-2.5.0a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-Gnt4Ck' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8788404/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- rna-star_2.5.0a+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-tZbDeA/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/<>/resolver-tZbDeA/apt_archive ./ InRelease Ign:1 file:/<>/resolver-tZbDeA/apt_archive ./ InRelease Get:2 file:/<>/resolver-tZbDeA/apt_archive ./ Release [2119 B] Get:2 file:/<>/resolver-tZbDeA/apt_archive ./ Release [2119 B] Get:3 file:/<>/resolver-tZbDeA/apt_archive ./ Release.gpg Ign:3 file:/<>/resolver-tZbDeA/apt_archive ./ Release.gpg Get:4 file:/<>/resolver-tZbDeA/apt_archive ./ Sources [214 B] Get:5 file:/<>/resolver-tZbDeA/apt_archive ./ Packages [526 B] Ign:4 file:/<>/resolver-tZbDeA/apt_archive ./ Sources Get:4 file:/<>/resolver-tZbDeA/apt_archive ./ Sources [214 B] Ign:5 file:/<>/resolver-tZbDeA/apt_archive ./ Packages Get:5 file:/<>/resolver-tZbDeA/apt_archive ./ Packages [526 B] Reading package lists... W: The repository 'file:/<>/resolver-tZbDeA/apt_archive ./ Release' is not signed. Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 file:/<>/resolver-tZbDeA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12018 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-94Cfbc/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. Get:1 file:/<>/resolver-94Cfbc/apt_archive ./ InRelease Ign:1 file:/<>/resolver-94Cfbc/apt_archive ./ InRelease Get:2 file:/<>/resolver-94Cfbc/apt_archive ./ Release [2119 B] Get:2 file:/<>/resolver-94Cfbc/apt_archive ./ Release [2119 B] Get:3 file:/<>/resolver-94Cfbc/apt_archive ./ Release.gpg Ign:3 file:/<>/resolver-94Cfbc/apt_archive ./ Release.gpg Get:4 file:/<>/resolver-94Cfbc/apt_archive ./ Sources [232 B] Get:5 file:/<>/resolver-94Cfbc/apt_archive ./ Packages [552 B] Ign:4 file:/<>/resolver-94Cfbc/apt_archive ./ Sources Get:4 file:/<>/resolver-94Cfbc/apt_archive ./ Sources [232 B] Ign:5 file:/<>/resolver-94Cfbc/apt_archive ./ Packages Get:5 file:/<>/resolver-94Cfbc/apt_archive ./ Packages [552 B] Reading package lists... W: The repository 'file:/<>/resolver-94Cfbc/apt_archive ./ Release' is not signed. Reading package lists... +------------------------------------------------------------------------------+ | Install rna-star build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf vim-common zlib1g-dev Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl vim | vim-gnome | vim-gtk | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common zlib1g-dev 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 15.0 MB/15.0 MB of archives. After this operation, 60.6 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-rna-star-dummy Authentication warning overridden. Get:1 file:/<>/resolver-94Cfbc/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [794 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main s390x groff-base s390x 1.22.3-4 [1199 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main s390x bsdmainutils s390x 9.0.6ubuntu1 [178 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main s390x libpipeline1 s390x 1.4.1-1 [24.7 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main s390x man-db s390x 2.7.5-1 [850 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main s390x libmagic1 s390x 1:5.25-2ubuntu1 [214 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main s390x file s390x 1:5.25-2ubuntu1 [21.5 kB] Get:8 http://ftpmaster.internal/ubuntu xenial-proposed/main s390x vim-common s390x 2:7.4.826-1ubuntu2 [103 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main s390x libasprintf0v5 s390x 0.19.6-1ubuntu1 [6856 B] Get:10 http://ftpmaster.internal/ubuntu xenial/main s390x gettext-base s390x 0.19.6-1ubuntu1 [48.4 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main s390x libglib2.0-0 s390x 2.47.3-3 [1041 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main s390x libicu55 s390x 55.1-6ubuntu1 [7478 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main s390x libxml2 s390x 2.9.2+zdfsg1-4ubuntu2 [641 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main s390x libcroco3 s390x 0.6.11-1 [76.5 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main s390x libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main s390x gettext s390x 0.19.6-1ubuntu1 [1047 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main s390x po-debconf all 1.0.18 [234 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main s390x libarchive-zip-perl all 1.55-1 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main s390x libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main s390x dh-strip-nondeterminism all 0.014-1 [5596 B] Get:23 http://ftpmaster.internal/ubuntu xenial/main s390x debhelper all 9.20151126ubuntu1 [741 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/universe s390x libhts1 s390x 1.2.1-2ubuntu1 [213 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/universe s390x libhts-dev s390x 1.2.1-2ubuntu1 [269 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/main s390x zlib1g-dev s390x 1:1.2.8.dfsg-2ubuntu4 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.0 MB in 5s (2881 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12018 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-4_s390x.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_s390x.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../libpipeline1_1.4.1-1_s390x.deb ... 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Unpacking sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up groff-base (1.22.3-4) ... Setting up bsdmainutils (9.0.6ubuntu1) ... 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 libpipeline1:s390x (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmagic1:s390x (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up vim-common (2:7.4.826-1ubuntu2) ... Setting up libasprintf0v5:s390x (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:s390x (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:s390x (55.1-6ubuntu1) ... Setting up libxml2:s390x (2.9.2+zdfsg1-4ubuntu2) ... Setting up libcroco3:s390x (0.6.11-1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up gettext (0.19.6-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.55-1) ... Setting up libfile-stripnondeterminism-perl (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libhts1:s390x (1.2.1-2ubuntu1) ... Setting up libhts-dev:s390x (1.2.1-2ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.8.dfsg-2ubuntu4) ... Setting up debhelper (9.20151126ubuntu1) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.014-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.3.0-2-generic s390x (s390x) Toolchain package versions: binutils_2.25.90.20151211-0ubuntu2 dpkg-dev_1.18.3ubuntu1 g++-5_5.3.1-4ubuntu1 gcc-5_5.3.1-4ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-4ubuntu1 libstdc++6_5.3.1-4ubuntu1 linux-libc-dev_4.3.0-5.16 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.10 apt-transport-https_1.1.10 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.90.20151211-0ubuntu2 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.3.1-4ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.110-1ubuntu2 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 g++_4:5.2.1-16ubuntu2 g++-5_5.3.1-4ubuntu1 gcc_4:5.2.1-16ubuntu2 gcc-5_5.3.1-4ubuntu1 gcc-5-base_5.3.1-4ubuntu1 gettext_0.19.6-1ubuntu1 gettext-base_0.19.6-1ubuntu1 gnupg_1.4.19-6ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu9 libapt-pkg4.16_1.0.10.2ubuntu1 libapt-pkg5.0_1.1.10 libarchive-zip-perl_1.55-1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.6-1ubuntu1 libatomic1_5.3.1-4ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu5 libc-dev-bin_2.21-0ubuntu5 libc6_2.21-0ubuntu5 libc6-dev_2.21-0ubuntu5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-4ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu2 libdpkg-perl_1.18.3ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.3.1-4ubuntu1 libgcc1_1:5.3.1-4ubuntu1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.3-3 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.3.1-4ubuntu1 libgpg-error0_1.21-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhts-dev_1.2.1-2ubuntu1 libhts1_1.2.1-2ubuntu1 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl15_0.15-3 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu3 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libperl5.22_5.22.1-3 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libprocps4_2:3.3.10-4ubuntu1 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2e-1ubuntu1 libstdc++-5-dev_5.3.1-4ubuntu1 libstdc++6_5.3.1-4ubuntu1 libsystemd0_228-2ubuntu2 libtasn1-6_4.7-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2ubuntu1 libudev1_228-2ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4ubuntu2 linux-libc-dev_4.3.0-5.16 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu5 ncurses-base_6.0+20151024-2ubuntu1 ncurses-bin_6.0+20151024-2ubuntu1 openssl_1.0.2e-1ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.22.1-3 perl-base_5.22.1-3 perl-modules-5.22_5.22.1-3 pkg-create-dbgsym_0.70 pkgbinarymangler_125 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu1 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-2ubuntu2 systemd-sysv_228-2ubuntu2 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-2ubuntu2 util-linux_2.27.1-1ubuntu3 vim-common_2:7.4.826-1ubuntu2 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Dec 31 11:53:05 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./rna-star_2.5.0a+dfsg-1.dsc dpkg-source: info: extracting rna-star in rna-star-2.5.0a+dfsg dpkg-source: info: unpacking rna-star_2.5.0a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.5.0a+dfsg-1.debian.tar.xz dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying compilationstuff.patch dpkg-source: info: applying mips_shm_noreserve.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/rna-star-2.5.0a+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/rna-star-2.5.0a+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: source package rna-star dpkg-buildpackage: source version 2.5.0a+dfsg-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build rna-star-2.5.0a+dfsg dpkg-buildpackage: host architecture s390x fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.5.0a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.5.0a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.5.0a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.5.0a+dfsg' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.5.0a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -Wl,-z,relro" make[2]: Entering directory '/<>/rna-star-2.5.0a+dfsg/source' Makefile:85: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo BAMfunctions.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp STAR.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp ReadAlign.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp genomeParametersWrite.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp SequenceFuns.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp extendAlign.cpp bam_cat.c BAMfunctions.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp STAR.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp ReadAlign.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp genomeParametersWrite.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp SequenceFuns.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp extendAlign.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:01 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMfunctions.cpp OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp ReadAlign_quantTranscriptome.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Stats.cpp STAR.cpp sjdbPrepare.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp ReadAlign.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp genomeParametersWrite.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp SequenceFuns.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp extendAlign.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' SharedMemory.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' PackedArray.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' SuffixArrayFuns.cpp SuffixArrayFuns.cpp:191:82: warning: unused parameter 'dirR' [-Wunused-parameter] uint suffixArraySearch(char** s2, uint S, uint N, char* G, PackedArray& SA, bool dirR, uint i1, uint i2, uint L, Parameters* P) { ^ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome1(char**, long long unsigned int, long long unsigned int, long long unsigned int, char*, PackedArray&, long long unsigned int, bool, long long unsigned int, int&, Parameters*)': SuffixArrayFuns.cpp:358:1: warning: control reaches end of non-void function [-Wreturn-type] }; ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' STAR.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Parameters.cpp Parameters.cpp: In member function 'void Parameters::inputParameters(int, char**)': Parameters.cpp:1075:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int ii=0; iioutSAMattrOrder.size();ii++) { ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_outputTranscriptSJ.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_assignAlignToWindow.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_oneRead.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_stitchWindowSeeds.cpp ReadAlign_stitchWindowSeeds.cpp:255:1: warning: multi-line comment [-Wcomment] // if ( trA.canonSJ[isj]>=0 && \ ^ ReadAlign_stitchWindowSeeds.cpp: In member function 'void ReadAlign::stitchWindowSeeds(long long unsigned int, long long unsigned int, char*, char*, char*)': ReadAlign_stitchWindowSeeds.cpp:132:18: warning: unused variable 'iS1' [-Wunused-variable] uint iS1=seedChain[seedN-1]; ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_chimericDetection.cpp ReadAlign_chimericDetection.cpp: In member function 'bool ReadAlign::chimericDetection()': ReadAlign_chimericDetection.cpp:345:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bamIrepr=( (itr%2)==(trChim[itr].Str) && chimType!=3) ? bamN+1 : bamN;//this is the mate that is chimerically split ^ ReadAlign_chimericDetection.cpp:347:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] alignType=( (itr%2)==(trChim[itr].Str) ) ? -12 : -11; //right:left chimeric junction ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' stitchWindowAligns.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' extendAlign.cpp extendAlign.cpp: In function 'bool extendAlign(char*, char*, char*, long long unsigned int, long long unsigned int, int, int, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, double, bool, Transcript*)': extendAlign.cpp:26:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((gStart+iG)==-1 || G[iG]==5) {//prohibit extension through chr boundary ^ extendAlign.cpp:64:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((gStart+iG)==-1 || G[iG]==5 || R[iS]==MARK_FRAG_SPACER_BASE) break; //no extension through chr boundary, or through the spacer between fragments ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' stitchAlignToTranscript.cpp stitchAlignToTranscript.cpp:376:1: warning: multi-line comment [-Wcomment] // if ( extendAlign(R, Q, G, rBstart-1, gBstart-1, -1, -1, gBstart-trA->exons[0][EX_G]+trA->exons[0][EX_R], trA->nMatch, trA->nMM, outFilterMismatchNmaxTotal, P->outFilterMismatchNoverLmax, \ ^ stitchAlignToTranscript.cpp: In function 'int stitchAlignToTranscript(long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, Parameters*, char*, char*, char*, Transcript*, long long unsigned int)': stitchAlignToTranscript.cpp:302:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] && ( jCan<0 || (jCan<7 && nMM<=P->alignSJstitchMismatchNmax[(jCan+1)/2]) ) ) ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' alignSmithWaterman.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' genomeGenerate.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' genomeParametersWrite.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' genomeScanFastaFiles.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' genomeSAindex.cpp genomeSAindex.cpp: In function 'void genomeSAindexChunk(char*, PackedArray&, Parameters*, PackedArray&, long long unsigned int, long long unsigned int)': genomeSAindex.cpp:183:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( iL==iL4 ) {//this suffix contains N and does not belong in SAi ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Genome_insertSequences.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' insertSeqSA.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' funCompareUintAndSuffixes.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' TimeFunctions.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ErrorWarning.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' loadGTF.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' streamFuns.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' stringSubstituteAll.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Transcriptome.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Transcriptome_quantAlign.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_quantTranscriptome.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Quantifications.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneCountsAddAlign.cpp: In member function 'void Transcriptome::geneCountsAddAlign(long long unsigned int, Transcript**)': Transcriptome_geneCountsAddAlign.cpp:47:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } else if (gene1.at(itype)!=exG.g[e1]) {//another gene overlaps this read ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' sjdbLoadFromFiles.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' sjdbLoadFromStream.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' sjdbPrepare.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' sjdbBuildIndex.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' sjdbInsertJunctions.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' mapThreadsSpawn.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' BAMoutput.cpp g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' BAMfunctions.cpp BAMfunctions.cpp: In function 'int bam_read1_fromArray(char*, bam1_t*)': BAMfunctions.cpp:32:21: warning: unused variable 'ret' [-Wunused-variable] int32_t block_len, ret, i; ^ BAMfunctions.cpp:32:26: warning: unused variable 'i' [-Wunused-variable] int32_t block_len, ret, i; ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' ReadAlign_alignBAM.cpp ReadAlign_alignBAM.cpp: In instantiation of 'int bamAttrArrayWriteInt(intType, const char*, char*, Parameters*) [with intType = long long unsigned int]': ReadAlign_alignBAM.cpp:194:78: required from here ReadAlign_alignBAM.cpp:92:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (x >= -127) { ^ ReadAlign_alignBAM.cpp:94:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } else if (x >= -32767) { ^ ReadAlign_alignBAM.cpp:98:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (!(x>=-2147483647)) { ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp:6:104: warning: unused parameter 'bgzfBAM' [-Wunused-parameter] void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) { ^ g++ -c -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:04 UTC 2015 :/<>/rna-star-2.5.0a+dfsg/source"' signalFromBAM.cpp signalFromBAM.cpp: In function 'void signalFromBAM(std::__cxx11::string, std::__cxx11::string, Parameters)': signalFromBAM.cpp:63:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (uint32_t is=0;is "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ^ signalFromBAM.cpp: In function 'signalFromBAM.constprop': signalFromBAM.cpp:175:29: warning: 'chrLen' may be used uninitialized in this function [-Wmaybe-uninitialized] if (aG>=chrLen) { ^ signalFromBAM.cpp:77:18: note: 'chrLen' was declared here uint32_t chrLen; ^ Parameters_openReadsFiles.cpp: In member function 'openReadsFiles': Parameters_openReadsFiles.cpp:30:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] for (uint imate=0;imate>/rna-star-2.5.0a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.5.0a+dfsg' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/rna-star-2.5.0a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/rna-star-2.5.0a+dfsg' dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: rna-star dh_strip debug symbol extraction: packages to act on: rna-star dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: rna-star dh_gencontrol debug symbol wrapper: packages to act on: rna-star dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package rna-star (pkgdir debian/rna-star, ddeb package dir debian/rna-star-dbgsym) dh_gencontrol debug symbol wrapper: building rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 125 pkgstriptranslations: processing rna-star (in debian/rna-star); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/rna-star/DEBIAN/control, package rna-star, directory debian/rna-star DEBUG: wait rna-star 1:rna-star DEBUG: clear rna-star 1:rna-star DEBUG: done rna-star pkgstripfiles: Running PNG optimization (using 4 cpus) for package rna-star ... pkgstripfiles: No PNG files. dpkg-deb: building package 'rna-star' in '../rna-star_2.5.0a+dfsg-1_s390x.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../rna-star_2.5.0a+dfsg-1_s390x.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build rna-star-2.5.0a+dfsg dpkg-buildpackage: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20151231-1710 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.5.0a+dfsg-1_s390x.changes: ------------------------------------- Format: 1.8 Date: Thu, 31 Dec 2015 12:41:06 +0100 Source: rna-star Binary: rna-star Architecture: s390x Version: 2.5.0a+dfsg-1 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.0a+dfsg-1) unstable; urgency=medium . * Packaging moved from svn to git * New upstream version Checksums-Sha1: 2461f18a1c4ca358dd7a18b03a22686798ba0d64 673934 rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb a6c60b94bbfb6a062509f51d7680cd52c8925e9a 339812 rna-star_2.5.0a+dfsg-1_s390x.deb Checksums-Sha256: 2a039fad58cf918d380146bd3cf4f94aeb86b21ad1a0d819ace14227bf86f01b 673934 rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb 7b24bd03b76fa3850ccbaa210af293bd621999def2e18aba4a7dc4fff21d0abb 339812 rna-star_2.5.0a+dfsg-1_s390x.deb Files: 236116eab1ab2de12a050d32ca505877 673934 science extra rna-star-dbgsym_2.5.0a+dfsg-1_s390x.ddeb 5d3a65e4d96eeed771573f1125ad1402 339812 science optional rna-star_2.5.0a+dfsg-1_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star_2.5.0a+dfsg-1_s390x.deb -------------------------------- new debian package, version 2.0. size 339812 bytes: control archive=1344 bytes. 1451 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.5.0a+dfsg-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 781 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.3.1), libgomp1 (>= 4.9), libhts1 (>= 1.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://code.google.com/p/rna-star/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2015-12-31 17:10 ./ drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/ drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/bin/ -rwxr-xr-x root/root 523280 2015-12-31 17:10 ./usr/bin/STAR drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/ drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2015-12-31 11:51 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2015-12-31 11:51 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3193 2015-11-07 19:01 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 2118 2015-11-07 19:01 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 249630 2015-11-07 19:01 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 435 2015-12-31 11:51 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 2444 2015-12-31 11:51 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-31 17:10 ./usr/share/man/man1/ -rw-r--r-- root/root 814 2015-12-31 17:10 ./usr/share/man/man1/STAR.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 20112 Build-Time: 55 Distribution: xenial-proposed Host Architecture: s390x Install-Time: 11 Job: rna-star_2.5.0a+dfsg-1.dsc Machine Architecture: s390x Package: rna-star Package-Time: 66 Source-Version: 2.5.0a+dfsg-1 Space: 20112 Status: successful Version: 2.5.0a+dfsg-1 -------------------------------------------------------------------------------- Finished at 20151231-1710 Build needed 00:01:06, 20112k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8788404'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8788404/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8788404'] Unmounting chroot for build PACKAGEBUILD-8788404... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8788404'] Removing build PACKAGEBUILD-8788404