RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-02 3.13.0-74-generic #118-Ubuntu SMP Thu Dec 17 22:52:10 UTC 2015 x86_64 Buildd toolchain package versions: launchpad-buildd_135 python-lpbuildd_135 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.5 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 31 Dec 17:08:36 ntpdate[1621]: adjust time server 10.211.37.1 offset -0.066455 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8788398', '/home/buildd/filecache-default/8204889cda79fca0b488b979ea0c52fb9d6dbd17'] Unpacking chroot for build PACKAGEBUILD-8788398 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8788398'] Mounting chroot for build PACKAGEBUILD-8788398 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8788398', '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-8788398 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8788398', 'amd64'] Updating debian chroot for build PACKAGEBUILD-8788398 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main amd64 Packages [1463 kB] Get:6 http://ftpmaster.internal xenial/universe amd64 Packages [7103 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [848 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4760 kB] Get:9 http://ftpmaster.internal xenial-security/main amd64 Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe amd64 Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main amd64 Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe amd64 Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main amd64 Packages [112 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe amd64 Packages [395 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [64.1 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [237 kB] Fetched 15.6 MB in 6s (2313 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'apt-get autoremove' to remove them. The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libisl15 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: advancecomp apt apt-transport-https base-files binutils bsdutils cpp cpp-5 debconf diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 liblsan0 libmount1 libmpfr4 libmpx0 libncurses5 libncursesw5 libp11-kit0 libpng12-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 110 upgraded, 5 newly installed, 1 to remove and 0 not upgraded. Need to get 137 MB of archives. After this operation, 365 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files amd64 9.4ubuntu3 [62.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils amd64 1:2.27.1-1ubuntu3 [51.5 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils amd64 1:3.3-3 [156 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg amd64 1.18.3ubuntu1 [2081 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev amd64 2.21-0ubuntu5 [1951 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin amd64 2.21-0ubuntu5 [68.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev amd64 4.3.0-5.16 [819 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 amd64 1:2.24-12 [12.9 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin amd64 2.21-0ubuntu5 [1172 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 amd64 5.3.1-4ubuntu1 [55.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libitm1 amd64 5.3.1-4ubuntu1 [27.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 amd64 5.3.1-4ubuntu1 [8888 B] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 amd64 5.3.1-4ubuntu1 [269 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main liblsan0 amd64 5.3.1-4ubuntu1 [109 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libtsan0 amd64 5.3.1-4ubuntu1 [249 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base amd64 5.3.1-4ubuntu1 [16.3 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 amd64 1:5.3.1-4ubuntu1 [38.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 amd64 5.3.1-4ubuntu1 [100 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcilkrts5 amd64 5.3.1-4ubuntu1 [40.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libmpx0 amd64 5.3.1-4ubuntu1 [9740 B] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main libquadmath0 amd64 5.3.1-4ubuntu1 [131 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 amd64 0.15-3 [514 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 amd64 5.3.1-4ubuntu1 [30.1 MB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 amd64 5.3.1-4ubuntu1 [38.8 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main binutils amd64 2.25.90.20151211-0ubuntu2 [2311 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 amd64 5.3.1-4ubuntu1 [32.3 MB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 amd64 5.3.1-4ubuntu1 [30.3 MB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev amd64 5.3.1-4ubuntu1 [2232 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev amd64 5.3.1-4ubuntu1 [1424 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 amd64 5.3.1-4ubuntu1 [393 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 amd64 2:6.1.0+dfsg-2 [240 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 amd64 3.1.3-2 [189 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libc6 amd64 2.21-0ubuntu5 [4789 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs amd64 1.42.13-1ubuntu1 [188 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs amd64 1.42.13-1ubuntu1 [771 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main findutils amd64 4.4.2-10 [281 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep amd64 2.22-1 [149 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main hostname amd64 3.16ubuntu2 [11.5 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main init amd64 1.24ubuntu2 [3966 B] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 amd64 2.27.1-1ubuntu3 [62.3 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 amd64 2.27.1-1ubuntu3 [14.7 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 amd64 2.27.1-1ubuntu3 [107 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 amd64 2.27.1-1ubuntu3 [139 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils amd64 2.88dsf-59.2ubuntu3 [25.7 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main initscripts amd64 2.88dsf-59.2ubuntu3 [24.8 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main util-linux amd64 2.27.1-1ubuntu3 [847 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 amd64 228-2ubuntu2 [56.6 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main udev amd64 228-2ubuntu2 [977 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 amd64 228-2ubuntu2 [203 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main systemd amd64 228-2ubuntu2 [3494 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 amd64 2.4-3 [56.0 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 amd64 6.0+20151024-2ubuntu1 [77.1 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 amd64 6.0+20151024-2ubuntu1 [93.9 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 amd64 6.0+20151024-2ubuntu1 [116 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 amd64 2:3.3.10-4ubuntu1 [32.8 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main procps amd64 2:3.3.10-4ubuntu1 [222 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapparmor1 amd64 2.10-0ubuntu9 [29.0 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 amd64 1:2.4.4-4ubuntu1 [36.3 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 amd64 2.27.1-1ubuntu3 [114 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 amd64 2.2.3-2ubuntu3 [35.0 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin amd64 1:2.24-12 [20.2 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main mount amd64 2.27.1-1ubuntu3 [121 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin amd64 6.0+20151024-2ubuntu1 [135 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-modules-5.22 all 5.22.1-3 [2648 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libperl5.22 amd64 5.22.1-3 [3322 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl amd64 5.22.1-3 [237 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-base amd64 5.22.1-3 [1281 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main tar amd64 1.28-2.1 [209 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 amd64 1.1.10 [680 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main apt amd64 1.1.10 [963 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main gpgv amd64 1.4.19-6ubuntu1 [165 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main gnupg amd64 1.4.19-6ubuntu1 [626 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv amd64 228-2ubuntu2 [15.1 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 amd64 3.2.1-4 [17.8 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libp11-kit0 amd64 0.23.2-3 [107 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 amd64 4.7-3 [43.1 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 amd64 3.3.18-1ubuntu1 [520 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libldap-2.4-2 amd64 2.4.41+dfsg-1ubuntu3 [160 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 amd64 1.42.13-1ubuntu1 [65.7 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 amd64 0.198ubuntu1 [6368 B] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 amd64 2:1.02.110-1ubuntu2 [145 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 amd64 1.21-1 [34.4 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 amd64 1.6.4-4 [336 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 amd64 2.4-2 [186 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:91 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 amd64 2.4-3 [79.3 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main libss2 amd64 1.42.13-1ubuntu1 [70.0 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support amd64 2.21-0ubuntu5 [7174 B] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 amd64 1.2.54-1 [116 kB] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 amd64 3.9.2-1 [395 kB] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 amd64 1.0.2e-1ubuntu1 [1080 kB] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup amd64 2:1.02.110-1ubuntu2 [59.8 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 amd64 1.13.2+dfsg-4 [120 kB] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 amd64 1.13.2+dfsg-4 [274 kB] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 amd64 1.13.2+dfsg-4 [30.4 kB] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 amd64 1.13.2+dfsg-4 [81.3 kB] Get:102 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 amd64 1.5.9-8ubuntu1 [9904 B] Get:103 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 amd64 1.32-3ubuntu1 [45.5 kB] Get:104 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls amd64 7.45.0-1ubuntu1 [183 kB] Get:105 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https amd64 1.1.10 [25.3 kB] Get:106 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 amd64 1.10.6-1ubuntu1 [161 kB] Get:107 http://ftpmaster.internal/ubuntu/ xenial/main openssl amd64 1.0.2e-1ubuntu1 [491 kB] Get:108 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp amd64 1.20-1 [160 kB] Get:109 http://ftpmaster.internal/ubuntu/ xenial/main cpp amd64 4:5.2.1-16ubuntu2 [27.6 kB] Get:110 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:111 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:112 http://ftpmaster.internal/ubuntu/ xenial/main gcc amd64 4:5.2.1-16ubuntu2 [5208 B] Get:113 http://ftpmaster.internal/ubuntu/ xenial/main g++ amd64 4:5.2.1-16ubuntu2 [1506 B] Get:114 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:115 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 137 MB in 25s (5312 kB/s) (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 ... 11690 files and directories currently installed.) Preparing to unpack .../base-files_9.4ubuntu3_amd64.deb ... Unpacking base-files (9.4ubuntu3) over (7.2ubuntu11) ... Setting up base-files (9.4ubuntu3) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... 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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 ... 11709 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_amd64.deb ... Unpacking libmount1:amd64 (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:amd64 (2.27.1-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Setting up libtsan0:amd64 (5.3.1-4ubuntu1) ... Setting up libubsan0:amd64 (5.3.1-4ubuntu1) ... Setting up libcilkrts5:amd64 (5.3.1-4ubuntu1) ... Setting up libmpx0:amd64 (5.3.1-4ubuntu1) ... Setting up libquadmath0:amd64 (5.3.1-4ubuntu1) ... Setting up libgmp10:amd64 (2:6.1.0+dfsg-2) ... Setting up libisl15:amd64 (0.15-3) ... Setting up libmpfr4:amd64 (3.1.3-2) ... Setting up cpp-5 (5.3.1-4ubuntu1) ... Setting up libcc1-0:amd64 (5.3.1-4ubuntu1) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgcc-5-dev:amd64 (5.3.1-4ubuntu1) ... Setting up gcc-5 (5.3.1-4ubuntu1) ... Setting up libstdc++-5-dev:amd64 (5.3.1-4ubuntu1) ... Setting up g++-5 (5.3.1-4ubuntu1) ... Setting up libprocps4:amd64 (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. virtio network devices detected, disabling predictable interface names in /etc/systemd/network/50-virtio-kernel-names.link Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up perl-modules-5.22 (5.22.1-3) ... Setting up libperl5.22:amd64 (5.22.1-3) ... Setting up perl (5.22.1-3) ... 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 libffi6:amd64 (3.2.1-4) ... Setting up libp11-kit0:amd64 (0.23.2-3) ... Setting up libtasn1-6:amd64 (4.7-3) ... Setting up libgnutls-deb0-28:amd64 (3.3.18-1ubuntu1) ... Setting up libldap-2.4-2:amd64 (2.4.41+dfsg-1ubuntu3) ... Setting up libpng12-0:amd64 (1.2.54-1) ... Setting up libsqlite3-0:amd64 (3.9.2-1) ... Setting up libssl1.0.0:amd64 (1.0.2e-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libkrb5support0:amd64 (1.13.2+dfsg-4) ... Setting up libk5crypto3:amd64 (1.13.2+dfsg-4) ... Setting up libkeyutils1:amd64 (1.5.9-8ubuntu1) ... Setting up libkrb5-3:amd64 (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-4) ... Setting up libidn11:amd64 (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.10) ... Setting up libdbus-1-3:amd64 (1.10.6-1ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... 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-8788398', 'amd64', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=xenial-proposed', '--purge=never', '--nolog', '-A', 'rna-star_2.5.0a+dfsg-1.dsc'] Initiating build PACKAGEBUILD-8788398 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.13.0-74-generic #118-Ubuntu SMP Thu Dec 17 22:52:10 UTC 2015 x86_64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lcy01-02.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ rna-star 2.5.0a+dfsg-1 (amd64) 31 Dec 2015 17:10 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: rna-star Version: 2.5.0a+dfsg-1 Source Version: 2.5.0a+dfsg-1 Distribution: xenial-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/rna-star-gdrU7E/rna-star-2.5.0a+dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/rna-star-gdrU7E' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8788398/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 '/«BUILDDIR»/resolver-dK90qR/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Packages [528 B] Ign:4 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ Packages [528 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-dK90qR/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 packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/770 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:/«BUILDDIR»/resolver-dK90qR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 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 ... 12305 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/«BUILDDIR»/resolver-rl262J/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Sources [440 B] Ign:4 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Sources Get:5 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Packages [706 B] Ign:5 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Sources [440 B] Get:5 file:/«BUILDDIR»/resolver-rl262J/apt_archive ./ Packages [706 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-rl262J/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 packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. 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 15.3 MB/15.3 MB of archives. After this operation, 59.2 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:/«BUILDDIR»/resolver-rl262J/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [950 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main amd64 groff-base amd64 1.22.3-4 [1143 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main amd64 bsdmainutils amd64 9.0.6ubuntu1 [175 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main amd64 libpipeline1 amd64 1.4.1-1 [24.9 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main amd64 man-db amd64 2.7.5-1 [854 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main amd64 libmagic1 amd64 1:5.25-2ubuntu1 [216 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main amd64 file amd64 1:5.25-2ubuntu1 [21.2 kB] Get:9 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 vim-common amd64 2:7.4.826-1ubuntu2 [103 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main amd64 libasprintf0v5 amd64 0.19.6-1ubuntu1 [6924 B] Get:11 http://ftpmaster.internal/ubuntu xenial/main amd64 gettext-base amd64 0.19.6-1ubuntu1 [48.6 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main amd64 libglib2.0-0 amd64 2.47.3-3 [1114 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main amd64 libicu55 amd64 55.1-6ubuntu1 [7643 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml2 amd64 2.9.2+zdfsg1-4ubuntu2 [696 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main amd64 libcroco3 amd64 0.6.11-1 [81.6 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main amd64 gettext amd64 0.19.6-1ubuntu1 [1063 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main amd64 po-debconf all 1.0.18 [234 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main amd64 libarchive-zip-perl all 1.55-1 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main amd64 libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main amd64 dh-strip-nondeterminism all 0.014-1 [5596 B] Get:23 http://ftpmaster.internal/ubuntu xenial/main amd64 debhelper all 9.20151126ubuntu1 [741 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/universe amd64 libhts1 amd64 1.2.1-2ubuntu1 [225 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/universe amd64 libhts-dev amd64 1.2.1-2ubuntu1 [276 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2ubuntu4 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.3 MB in 0s (19.8 MB/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 ... 12305 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-4_amd64.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_amd64.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_amd64.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package vim-common. Preparing to unpack .../vim-common_2%3a7.4.826-1ubuntu2_amd64.deb ... Unpacking vim-common (2:7.4.826-1ubuntu2) ... Selecting previously unselected package libasprintf0v5:amd64. Preparing to unpack .../libasprintf0v5_0.19.6-1ubuntu1_amd64.deb ... Unpacking libasprintf0v5:amd64 (0.19.6-1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.6-1ubuntu1_amd64.deb ... Unpacking gettext-base (0.19.6-1ubuntu1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.47.3-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.47.3-3) ... Selecting previously unselected package libicu55:amd64. Preparing to unpack .../libicu55_55.1-6ubuntu1_amd64.deb ... Unpacking libicu55:amd64 (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu2_amd64.deb ... Unpacking libxml2:amd64 (2.9.2+zdfsg1-4ubuntu2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.11-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.11-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.6-1ubuntu1_amd64.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:amd64 (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:amd64 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up vim-common (2:7.4.826-1ubuntu2) ... Setting up libasprintf0v5:amd64 (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:amd64 (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:amd64 (55.1-6ubuntu1) ... Setting up libxml2:amd64 (2.9.2+zdfsg1-4ubuntu2) ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.13.0-74-generic amd64 (x86_64) 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 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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 libcilkrts5_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 libdbus-1-3_1.10.6-1ubuntu1 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 libisl13_0.14-2 libisl15_0.15-3 libitm1_5.3.1-4ubuntu1 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 liblsan0_5.3.1-4ubuntu1 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 libmpx0_5.3.1-4ubuntu1 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4ubuntu27 libnih1_1.0.3-4ubuntu27 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 libquadmath0_5.3.1-4ubuntu1 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 libtsan0_5.3.1-4ubuntu1 libubsan0_5.3.1-4ubuntu1 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=/«BUILDDIR»/rna-star-2.5.0a+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/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 amd64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg' dh_clean debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/«BUILDDIR»/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 '/«BUILDDIR»/rna-star-2.5.0a+dfsg/source' Makefile:85: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_mapOneRead.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlignChunk.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.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 genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Transcript.cpp Genome_insertSequences.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.cpp bam_cat.c OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_mapOneRead.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlignChunk.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.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 genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Transcript.cpp Genome_insertSequences.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Dec 31 17:10:14 UTC 2015 :/«BUILDDIR»/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 OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_mapOneRead.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp GlobalVariables.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlignChunk.cpp Transcriptome.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.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 genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp Transcriptome_quantAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp stringSubstituteAll.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Transcript.cpp Genome_insertSequences.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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 17:10:21 UTC 2015 :/«BUILDDIR»/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()); ^ ReadAlign_alignBAM.cpp: In member function 'alignBAM.constprop': ReadAlign_alignBAM.cpp:375:34: warning: 'trimR1' may be used uninitialized in this function [-Wmaybe-uninitialized] seqMateLength-=trimR1; ^ ReadAlign_alignBAM.cpp:171:22: note: 'trimR1' was declared here uint trimL1, trimR1; ^ ReadAlign_alignBAM.cpp:371:34: warning: 'trimL1' may be used uninitialized in this function [-Wmaybe-uninitialized] seqMateLength-=trimL1; ^ ReadAlign_alignBAM.cpp:171:14: note: 'trimL1' was declared here uint trimL1, trimR1; ^ 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=chrLen) { ^ signalFromBAM.cpp:77:18: note: 'chrLen' was declared here uint32_t chrLen; ^ make[2]: Leaving directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg/source' make[1]: Leaving directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg' dh_auto_test fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/«BUILDDIR»/rna-star-2.5.0a+dfsg' dh_fixperms dh_strip 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 amd64: 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 dh_shlibdeps dh_installdeb dh_gencontrol 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 amd64: 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_amd64.ddeb dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.5.0a+dfsg-1_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile rna-star-dbgsym_2.5.0a+dfsg-1_amd64.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb 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_amd64.deb'. dpkg-genchanges -b -mLaunchpad Build Daemon >../rna-star_2.5.0a+dfsg-1_amd64.changes dpkg-genchanges: binary-only upload (no source code included) dpkg-source --after-build rna-star-2.5.0a+dfsg dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151231-1712 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ rna-star_2.5.0a+dfsg-1_amd64.changes: ───────────────────────────────────── Format: 1.8 Date: Thu, 31 Dec 2015 12:41:06 +0100 Source: rna-star Binary: rna-star Architecture: amd64 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: 2c59dc91daadaa1bcecbf2a60bc169238352cf70 744572 rna-star-dbgsym_2.5.0a+dfsg-1_amd64.ddeb a3210f97980827850c410835bbb463c29673a09a 347500 rna-star_2.5.0a+dfsg-1_amd64.deb Checksums-Sha256: 38b542b45e6e60697a78d20bdc8ba820e6211750b189d411166f38ca8dd80386 744572 rna-star-dbgsym_2.5.0a+dfsg-1_amd64.ddeb 9d6366926ae4f92b061a4150e8deb72edc54ff5d74a5c9f93cb1c949d2c20dd8 347500 rna-star_2.5.0a+dfsg-1_amd64.deb Files: 4a42399daeb98467d7c6fd7df92c03bf 744572 science extra rna-star-dbgsym_2.5.0a+dfsg-1_amd64.ddeb 2803706726262b3b7a82236705b78094 347500 science optional rna-star_2.5.0a+dfsg-1_amd64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ rna-star_2.5.0a+dfsg-1_amd64.deb ──────────────────────────────── new debian package, version 2.0. size 347500 bytes: control archive=1340 bytes. 1452 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.5.0a+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 776 Depends: libc6 (>= 2.14), 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 17:12 ./ drwxr-xr-x root/root 0 2015-12-31 17:12 ./usr/ drwxr-xr-x root/root 0 2015-12-31 17:12 ./usr/bin/ -rwxr-xr-x root/root 519016 2015-12-31 17:12 ./usr/bin/STAR drwxr-xr-x root/root 0 2015-12-31 17:12 ./usr/share/ drwxr-xr-x root/root 0 2015-12-31 17:12 ./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 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-31 17:12 ./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 17:12 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-31 17:12 ./usr/share/man/man1/ -rw-r--r-- root/root 814 2015-12-31 17:12 ./usr/share/man/man1/STAR.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 20404 Build-Time: 145 Distribution: xenial-proposed Host Architecture: amd64 Install-Time: 10 Job: rna-star_2.5.0a+dfsg-1.dsc Machine Architecture: amd64 Package: rna-star Package-Time: 156 Source-Version: 2.5.0a+dfsg-1 Space: 20404 Status: successful Version: 2.5.0a+dfsg-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151231-1712 Build needed 00:02:36, 20404k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8788398'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8788398/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8788398'] Unmounting chroot for build PACKAGEBUILD-8788398... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8788398'] Removing build PACKAGEBUILD-8788398