RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-24 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.11. Syncing the system clock with the buildd NTP service... 30 Apr 02:21:31 ntpdate[1783]: adjust time server 10.211.37.1 offset 0.020183 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12501013', '/home/buildd/filecache-default/e3a0751dad18cad81698aa46cb02fd9a2acf7c0b'] Unpacking chroot for build PACKAGEBUILD-12501013 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12501013'] Mounting chroot for build PACKAGEBUILD-12501013 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12501013', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12501013 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12501013', 'amd64'] Updating debian chroot for build PACKAGEBUILD-12501013 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 Packages [1176 kB] Get:6 http://ftpmaster.internal/ubuntu artful/universe amd64 Packages [8105 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4682 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 Packages [72.0 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [36.3 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/universe amd64 Packages [254 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [161 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/multiverse amd64 Packages [972 B] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/multiverse Translation-en [544 B] Fetched 14.9 MB in 3s (4827 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: advancecomp debianutils libapparmor1 libsystemd0 libudev1 libusb-0.1-4 systemd systemd-sysv 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3058 kB of archives. After this operation, 561 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 debianutils amd64 4.8.1.1 [85.6 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapparmor1 amd64 2.11.0-2ubuntu5 [30.1 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd amd64 233-5ubuntu1 [2443 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libsystemd0 amd64 233-5ubuntu1 [213 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 systemd-sysv amd64 233-5ubuntu1 [13.7 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libudev1 amd64 233-5ubuntu1 [58.2 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 advancecomp amd64 1.23-1 [197 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libusb-0.1-4 amd64 2:0.1.12-31 [17.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3058 kB in 0s (17.8 MB/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 ... 12466 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.1.1_amd64.deb ... Unpacking debianutils (4.8.1.1) over (4.8.1) ... Setting up debianutils (4.8.1.1) ... (Reading database ... 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Unpacking systemd (233-5ubuntu1) over (232-21ubuntu3) ... dpkg: warning: unable to delete old directory '/etc/dbus-1/system.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/dbus-1': Directory not empty Preparing to unpack .../libsystemd0_233-5ubuntu1_amd64.deb ... Unpacking libsystemd0:amd64 (233-5ubuntu1) over (232-21ubuntu3) ... Setting up libsystemd0:amd64 (233-5ubuntu1) ... Setting up libapparmor1:amd64 (2.11.0-2ubuntu5) ... Setting up systemd (233-5ubuntu1) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.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 ... 12492 files and directories currently installed.) Preparing to unpack .../systemd-sysv_233-5ubuntu1_amd64.deb ... Unpacking systemd-sysv (233-5ubuntu1) over (232-21ubuntu3) ... Preparing to unpack .../libudev1_233-5ubuntu1_amd64.deb ... Unpacking libudev1:amd64 (233-5ubuntu1) over (232-21ubuntu3) ... Setting up libudev1:amd64 (233-5ubuntu1) ... (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 ... 12492 files and directories currently installed.) Preparing to unpack .../advancecomp_1.23-1_amd64.deb ... Unpacking advancecomp (1.23-1) over (1.20-1) ... Preparing to unpack .../libusb-0.1-4_2%3a0.1.12-31_amd64.deb ... Unpacking libusb-0.1-4:amd64 (2:0.1.12-31) over (2:0.1.12-30) ... Setting up systemd-sysv (233-5ubuntu1) ... Setting up advancecomp (1.23-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up libusb-0.1-4:amd64 (2:0.1.12-31) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12501013', 'amd64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=artful-proposed', '--purge=never', '--nolog', '-A', 'trnascan-se_1.3.1-1.dsc'] Initiating build PACKAGEBUILD-12501013 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-24.buildd +==============================================================================+ | trnascan-se 1.3.1-1 (amd64) 30 Apr 2017 02:21 | +==============================================================================+ Package: trnascan-se Version: 1.3.1-1 Source Version: 1.3.1-1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/trnascan-se-V5wmnI/trnascan-se-1.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/trnascan-se-V5wmnI' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12501013/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- trnascan-se_1.3.1-1.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-LjGkkU/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-LjGkkU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-LjGkkU/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-LjGkkU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-LjGkkU/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-LjGkkU/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-LjGkkU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12492 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9) Filtered Build-Depends: debhelper (>= 9) dpkg-deb: building package 'sbuild-build-depends-trnascan-se-dummy' in '/<>/resolver-8i5Q2s/apt_archive/sbuild-build-depends-trnascan-se-dummy.deb'. Ign:1 copy:/<>/resolver-8i5Q2s/apt_archive ./ InRelease Get:2 copy:/<>/resolver-8i5Q2s/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-8i5Q2s/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-8i5Q2s/apt_archive ./ Sources [209 B] Get:5 copy:/<>/resolver-8i5Q2s/apt_archive ./ Packages [527 B] Fetched 2855 B in 0s (181 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install trnascan-se build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-trnascan-se-dummy 0 upgraded, 30 newly installed, 1 to remove and 0 not upgraded. Need to get 16.3 MB of archives. After this operation, 61.5 MB of additional disk space will be used. Get:1 copy:/<>/resolver-8i5Q2s/apt_archive ./ sbuild-build-depends-trnascan-se-dummy 0.invalid.0 [782 B] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 groff-base amd64 1.22.3-9 [1144 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main amd64 libbsd0 amd64 0.8.3-1 [41.4 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 bsdmainutils amd64 9.0.12ubuntu1 [177 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 libpipeline1 amd64 1.4.1-2 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main amd64 man-db amd64 2.7.6.1-2 [895 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libmagic-mgc amd64 1:5.30-1 [181 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libmagic1 amd64 1:5.30-1 [68.5 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 file amd64 1:5.30-1 [21.8 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main amd64 gettext-base amd64 0.19.8.1-2ubuntu1 [48.7 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main amd64 libglib2.0-0 amd64 2.52.0-1 [1144 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libicu57 amd64 57.1-6 [7690 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2 [698 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main amd64 libsigsegv2 amd64 2.10-5 [14.1 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main amd64 autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main amd64 autotools-dev all 20161112.1 [39.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main amd64 automake all 1:1.15-5ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main amd64 autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 dh-autoreconf all 14 [15.5 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 libfile-stripnondeterminism-perl all 0.032-1 [12.9 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 dh-strip-nondeterminism all 0.032-1 [4894 B] Get:26 http://ftpmaster.internal/ubuntu artful/main amd64 libcroco3 amd64 0.6.11-3 [80.9 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main amd64 gettext amd64 0.19.8.1-2ubuntu1 [1083 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main amd64 debhelper all 10.2.5ubuntu2 [870 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.3 MB in 0s (34.7 MB/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 ... 12492 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... 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 ... 12483 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.12ubuntu1_amd64.deb ... Unpacking bsdmainutils (9.0.12ubuntu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../06-libmagic1_1%3a5.30-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.30-1) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.30-1_amd64.deb ... Unpacking file (1:5.30-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.19.8.1-2ubuntu1_amd64.deb ... Unpacking gettext-base (0.19.8.1-2ubuntu1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../09-libglib2.0-0_2.52.0-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.52.0-1) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../10-libicu57_57.1-6_amd64.deb ... Unpacking libicu57:amd64 (57.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../11-libxml2_2.9.4+dfsg1-2.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-2.2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.10-5_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-1_amd64.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20161112.1_all.deb ... Unpacking autotools-dev (20161112.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15-5ubuntu1_all.deb ... Unpacking automake (1:1.15-5ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-2ubuntu1_all.deb ... Unpacking autopoint (0.19.8.1-2ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-2_all.deb ... Unpacking libtool (2.4.6-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_14_all.deb ... Unpacking dh-autoreconf (14) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_0.032-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.032-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../22-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_0.032-1_all.deb ... Unpacking dh-strip-nondeterminism (0.032-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../24-libcroco3_0.6.11-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.11-3) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-2ubuntu1_amd64.deb ... Unpacking gettext (0.19.8.1-2ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.2.5ubuntu2_all.deb ... Unpacking debhelper (10.2.5ubuntu2) ... Selecting previously unselected package sbuild-build-depends-trnascan-se-dummy. Preparing to unpack .../29-sbuild-build-depends-trnascan-se-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-trnascan-se-dummy (0.invalid.0) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.52.0-1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.11-3) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 autopoint (0.19.8.1-2ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.032-1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-5ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.032-1) ... Setting up debhelper (10.2.5ubuntu2) ... Setting up sbuild-build-depends-trnascan-se-dummy (0.invalid.0) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14308 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-75-generic amd64 (x86_64) Toolchain package versions: binutils_2.28-4ubuntu1 dpkg-dev_1.18.23ubuntu4 g++-6_6.3.0-14ubuntu3 gcc-6_6.3.0-14ubuntu3 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-14ubuntu3 libstdc++6_6.3.0-14ubuntu3 linux-libc-dev_4.10.0-20.22 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4.1ubuntu2 apt-transport-https_1.4.1ubuntu2 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-2ubuntu1 binutils_2.28-4ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-14ubuntu3 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Dec 14 07:48:58 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./trnascan-se_1.3.1-1.dsc dpkg-source: info: extracting trnascan-se in trnascan-se-1.3.1 dpkg-source: info: unpacking trnascan-se_1.3.1.orig.tar.gz dpkg-source: info: unpacking trnascan-se_1.3.1-1.debian.tar.xz dpkg-source: info: applying install-location.patch dpkg-source: info: applying perl5dir.patch dpkg-source: info: applying cflags.patch dpkg-source: info: applying ldflags.patch dpkg-source: info: applying manpage-errors.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package trnascan-se dpkg-buildpackage: info: source version 1.3.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build trnascan-se-1.3.1 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make -j4 clean make[1]: Entering directory '/<>' rm -f *.o *~ Makefile.bak core testrun.out \ trnascan-1.4 covels-SE coves-SE eufindtRNA reformat revcomp seqstat shuffle covea coveb covee covet covels coves structcheck mpcovels tRNAscan-SE instman make[1]: Leaving directory '/<>' dh_clean -O--parallel debian/rules build dh build --parallel dh_testdir -O--parallel dh_update_autotools_config -O--parallel dh_auto_configure -O--parallel dh_auto_build -O--parallel make -j4 make[1]: Entering directory '/<>' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c trnascan.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c align.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c dbviterbi.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c debug.c -Wl,-Bsymbolic-functions -Wl,-z,relro trnascan.c:335:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main(int argc, char **argv) ^~~~ trnascan.c: In function ‘main’: trnascan.c:433:16: warning: implicit declaration of function ‘getopt’ [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) ^~~~~~ trnascan.c: At top level: trnascan.c:1421:1: warning: return type defaults to ‘int’ [-Wimplicit-int] myindex (char *s, char *t) ^~~~~~~ trnascan.c: In function ‘fgetseq’: trnascan.c:1252:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, fpi); ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c emit.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c fast-dbviterbi.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c fastmodelmaker.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c konings.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c lengthdist.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c maxmodelmaker.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c misc.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c model.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c modelmaking.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c prior.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c probify.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c save.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c smallviterbi.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c scorestack.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c structs.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c trace.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c viterbi.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c alignio.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c sqerror.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c sqio.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c iupac.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c msf.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c revcomp.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c selex.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c sre_ctype.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c sre_math.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c sre_string.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c stack.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c types.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c gnuregex.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c interleaved.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c getopt.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c scan_main.c -Wl,-Bsymbolic-functions -Wl,-z,relro gnuregex.c: In function ‘re_match_2’: gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c score_main.c -Wl,-Bsymbolic-functions -Wl,-z,relro scan_main.c: In function ‘main’: scan_main.c:100:18: warning: implicit declaration of function ‘getopt’ [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ score_main.c: In function ‘main’: score_main.c:87:18: warning: implicit declaration of function ‘getopt’ [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c pavesi.c -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -c eufind_main.c -Wl,-Bsymbolic-functions -Wl,-z,relro /usr/bin/perl checkversion.pl sed 's#/tmp#/tmp#g' tRNAscan-SE.src | \ sed 's#bindir = ""#bindir =\"/usr/bin/"#g' | \ sed 's#/usr/local/lib/tRNAscanSE#/usr/share/tRNAscan-SE#g' | \ sed 's#version = ""#version = "1.3.1"#' | \ sed 's#release_date = ""#release_date = "January 2012"#' | \ sed 's#/usr/bin/perl#/usr/bin/perl#' > tRNAscan-SE sed 's#/usr/bin/perl#/usr/bin/perl#' instman.pl > instman sed 's#/usr/bin/perl#/usr/bin/perl#' sstofa.pl > sstofa tRNAscan-SE built The file "setup.tRNAscan-SE" has been created. If you type "source setup.tRNAscan-SE; rehash", the paths in your environment will be updated for this session. eufind_main.c: In function ‘main’: To update your environment upon every login, you should eufind_main.c:106:21: warning: implicit declaration of function ‘getopt’ [-Wimplicit-function-declaration] while ((optchar = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ add the line: source /<>/setup.tRNAscan-SE eufind_main.c:168:17: warning: implicit declaration of function ‘IntEncodeSeq’ [-Wimplicit-function-declaration] if (errno = IntEncodeSeq(iseq,seq,sqinfo.len)) ^~~~~~~~~~~~ eufind_main.c:175:7: warning: implicit declaration of function ‘Init_tRNA’ [-Wimplicit-function-declaration] Init_tRNA(prev_tRNA); /* clear previous tRNA */ ^~~~~~~~~ to your ".cshrc" file. eufind_main.c:194:14: warning: implicit declaration of function ‘GetBbox’ [-Wimplicit-function-declaration] while (GetBbox(&FirstScore,&seqidx,iseq,sqinfo.len,strand, ^~~~~~~ If you prefer to manually update your environment variables, eufind_main.c:204:10: warning: implicit declaration of function ‘GetSecABox’ [-Wimplicit-function-declaration] && (GetSecABox(tRNA,seq))){ ^~~~~~~~~~ be sure to make the following changes: eufind_main.c:206:9: warning: implicit declaration of function ‘GetBestTrxTerm’ [-Wimplicit-function-declaration] if (!GetBestTrxTerm(tRNA,seq,sqinfo.len,NoTermPenalty) && ^~~~~~~~~~~~~~ eufind_main.c:218:4: warning: implicit declaration of function ‘GetBestABox’ [-Wimplicit-function-declaration] GetBestABox(tRNA,seq,iseq,sqinfo.len,strand,ShowScores, ^~~~~~~~~~~ 1) Add /usr/bin to your PATH variable eufind_main.c:239:2: warning: implicit declaration of function ‘Get_tRNA_stats’ [-Wimplicit-function-declaration] Get_tRNA_stats(tRNA,seq,sqinfo.len,strand); ^~~~~~~~~~~~~~ 2) Add /usr/share/perl5 to your PERl5LIB variable eufind_main.c:241:6: warning: implicit declaration of function ‘tRNAOverlap’ [-Wimplicit-function-declaration] if (tRNAOverlap(tRNA,prev_tRNA,strand)) { ^~~~~~~~~~~ 3) Add /usr/share/man to your MANPATH variable eufind_main.c:258:6: warning: implicit declaration of function ‘Save_tRNA’ [-Wimplicit-function-declaration] Save_tRNA(prev_tRNA,&sqinfo,seq,strand,ShowScores,sqoffset); ^~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -DTSCANDIR=\"/usr/share/tRNAscan-SE\" -o trnascan-1.4 trnascan.c -Wl,-Bsymbolic-functions -Wl,-z,relro trnascan.c:335:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main(int argc, char **argv) ^~~~ trnascan.c: In function ‘main’: trnascan.c:433:16: warning: implicit declaration of function ‘getopt’ [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) ^~~~~~ trnascan.c: At top level: trnascan.c:1421:1: warning: return type defaults to ‘int’ [-Wimplicit-int] myindex (char *s, char *t) ^~~~~~~ trnascan.c: In function ‘fgetseq’: trnascan.c:1252:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, fpi); ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -DRELEASE="2.4.4" -DRELEASEDATE="January 2012" -o covels-SE scan_main.o align.o dbviterbi.o debug.o emit.o fast-dbviterbi.o fastmodelmaker.o konings.o lengthdist.o maxmodelmaker.o misc.o model.o modelmaking.o prior.o probify.o save.o smallviterbi.o scorestack.o structs.o trace.o viterbi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -DRELEASE="2.4.4" -DRELEASEDATE="January 2012" -o coves-SE score_main.o align.o dbviterbi.o debug.o emit.o fast-dbviterbi.o fastmodelmaker.o konings.o lengthdist.o maxmodelmaker.o misc.o model.o modelmaking.o prior.o probify.o save.o smallviterbi.o scorestack.o structs.o trace.o viterbi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm -Wl,-Bsymbolic-functions -Wl,-z,relro cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O -o eufindtRNA eufind_main.o \ pavesi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm -Wl,-Bsymbolic-functions -Wl,-z,relro make[1]: Leaving directory '/<>' dh_auto_test -O--parallel create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --parallel create-stamp debian/debhelper-build-stamp dh_testroot -O--parallel dh_prep -O--parallel dh_auto_install -O--parallel make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' . cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE /<>/debian/tmp/usr/bin/. cp -R tRNAscanSE /<>/debian/tmp/usr/share/perl5/ cp TPCsignal Dsignal *.cm gcode.* /<>/debian/tmp/usr/share/tRNAscan-SE/. cp tRNAscan-SE.man /<>/debian/tmp/usr/share/man/man1/tRNAscan-SE.1 make[1]: Leaving directory '/<>' dh_install -O--parallel dh_installdocs -O--parallel debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs Release.history make[1]: Leaving directory '/<>' dh_installman -O--parallel dh_perl -O--parallel dh_link -O--parallel dh_strip_nondeterminism -O--parallel dh_compress -O--parallel dh_fixperms -O--parallel dh_strip -O--parallel dh_makeshlibs -O--parallel dh_shlibdeps -O--parallel dh_installdeb -O--parallel dh_gencontrol -O--parallel dh_md5sums -O--parallel dh_builddeb -O--parallel INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing trnascan-se-dbgsym (in debian/.debhelper/trnascan-se/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing trnascan-se-common (in debian/trnascan-se-common); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/trnascan-se/dbgsym-root/DEBIAN/control, package trnascan-se-dbgsym, directory debian/.debhelper/trnascan-se/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package trnascan-se-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'trnascan-se-dbgsym' in 'debian/.debhelper/scratch-space/build-trnascan-se/trnascan-se-dbgsym_1.3.1-1_amd64.deb'. pkgstripfiles: processing control file: debian/trnascan-se-common/DEBIAN/control, package trnascan-se-common, directory debian/trnascan-se-common .. removing usr/share/doc/trnascan-se-common/changelog.gz INFO: pkgstripfiles: waiting for lock (trnascan-se-common) ... Renaming trnascan-se-dbgsym_1.3.1-1_amd64.deb to trnascan-se-dbgsym_1.3.1-1_amd64.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing trnascan-se (in debian/trnascan-se); do_strip: , oemstrip: INFO: pkgstripfiles: waiting for lock (trnascan-se-common) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/trnascan-se/DEBIAN/control, package trnascan-se, directory debian/trnascan-se .. removing usr/share/doc/trnascan-se/changelog.gz Skipping arch: any to arch: all dependency to trnascan-se-common pkgstripfiles: Running PNG optimization (using 4 cpus) for package trnascan-se ... pkgstripfiles: No PNG files. dpkg-deb: building package 'trnascan-se' in '../trnascan-se_1.3.1-1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package trnascan-se-common ... pkgstripfiles: No PNG files. dpkg-deb: building package 'trnascan-se-common' in '../trnascan-se-common_1.3.1-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../trnascan-se_1.3.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build trnascan-se-1.3.1 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170430-0222 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ trnascan-se_1.3.1-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 13 Dec 2016 23:35:18 -0800 Source: trnascan-se Binary: trnascan-se trnascan-se-common Architecture: all amd64 Version: 1.3.1-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Afif Elghraoui Description: trnascan-se - detection of transfer RNA genes in genomic sequence trnascan-se-common - detection of transfer RNA genes in genomic sequence (common files Closes: 803542 Changes: trnascan-se (1.3.1-1) unstable; urgency=medium . * Initial release (Closes: #803542) Checksums-Sha1: 2b72f39c60bf76897cc489f90300356fde4f6b53 89574 trnascan-se-common_1.3.1-1_all.deb 04a24d69f8061e86fe777151c65cf2f1fc2c805f 398024 trnascan-se-dbgsym_1.3.1-1_amd64.ddeb 32add6539faf0ad7f1636f92dd0e7c66c03edaf0 5286 trnascan-se_1.3.1-1_amd64.buildinfo 5ed27c01f1a11f523a67aa5038464c86529b6c4a 140142 trnascan-se_1.3.1-1_amd64.deb Checksums-Sha256: 976fb7af2e062e8f86e6b301fafd40af9a4848b76283f593a783c8665aeaa023 89574 trnascan-se-common_1.3.1-1_all.deb 90382a22c8fc1eb73123723bfb564127dfa85e398e76adbe4ccac3ade4bb9c0a 398024 trnascan-se-dbgsym_1.3.1-1_amd64.ddeb 234117bf692f65d60809e5a9407e949d598633f183b743f92edcab9fc22c7ac0 5286 trnascan-se_1.3.1-1_amd64.buildinfo 67f7a66d842bccbce05a681ac50504c0749b9ab1c3c77bbba0ea0f288562c490 140142 trnascan-se_1.3.1-1_amd64.deb Files: 164381acb4b42a94ecc48724c8f71e41 89574 non-free/science optional trnascan-se-common_1.3.1-1_all.deb ad19dbc9ae1840b8ddc8c7f136149131 398024 non-free/debug extra trnascan-se-dbgsym_1.3.1-1_amd64.ddeb 47bd9dfa97c6be1525f44613b338c00b 5286 non-free/science optional trnascan-se_1.3.1-1_amd64.buildinfo f6e0eb415f9db5a2940cf39bf556c563 140142 non-free/science optional trnascan-se_1.3.1-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ trnascan-se-common_1.3.1-1_all.deb ---------------------------------- new debian package, version 2.0. size 89574 bytes: control archive=2150 bytes. 1215 bytes, 23 lines control 3224 bytes, 45 lines md5sums Package: trnascan-se-common Source: trnascan-se Version: 1.3.1-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1161 Depends: perl Section: non-free/science Priority: optional Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Description: detection of transfer RNA genes in genomic sequence (common files) tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes. . This package contains the architecture-independent common files. drwxr-xr-x root/root 0 2016-12-14 07:35 ./ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/doc/trnascan-se-common/ -rw-r--r-- root/root 159 2016-12-14 07:35 ./usr/share/doc/trnascan-se-common/changelog.Debian.gz -rw-r--r-- root/root 2324 2016-12-14 07:21 ./usr/share/doc/trnascan-se-common/copyright drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/perl5/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/ -rw-r--r-- root/root 109745 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/CM.pm -rw-r--r-- root/root 2003 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Constants.pm -rw-r--r-- root/root 8756 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Eufind.pm -rw-r--r-- root/root 8047 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/GeneticCode.pm -rw-r--r-- root/root 1517 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/LogFile.pm -rw-r--r-- root/root 17603 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Options.pm -rw-r--r-- root/root 6184 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/SS.pm -rw-r--r-- root/root 20644 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/ScanResult.pm -rw-r--r-- root/root 24845 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Sequence.pm -rw-r--r-- root/root 11602 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Stats.pm -rw-r--r-- root/root 12802 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Tscan.pm -rw-r--r-- root/root 4575 2016-12-14 07:35 ./usr/share/perl5/tRNAscanSE/Utils.pm drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/tRNAscan-SE/ -rw-r--r-- root/root 14861 2016-12-14 07:35 ./usr/share/tRNAscan-SE/Archaea-BHB-noncan.cm -rw-r--r-- root/root 224 2016-12-14 07:35 ./usr/share/tRNAscan-SE/Dsignal -rw-r--r-- root/root 41083 2016-12-14 07:35 ./usr/share/tRNAscan-SE/ESELC.cm -rw-r--r-- root/root 34522 2016-12-14 07:35 ./usr/share/tRNAscan-SE/ESELCinf-c.cm -rw-r--r-- root/root 45507 2016-12-14 07:35 ./usr/share/tRNAscan-SE/PSELC.cm -rw-r--r-- root/root 36969 2016-12-14 07:35 ./usr/share/tRNAscan-SE/PSELCinf-c.cm -rw-r--r-- root/root 420 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TPCsignal -rw-r--r-- root/root 47403 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-arch.cm -rw-r--r-- root/root 59411 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-archns.cm -rw-r--r-- root/root 47403 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-bact.cm -rw-r--r-- root/root 59411 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-bactns.cm -rw-r--r-- root/root 45507 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-euk.cm -rw-r--r-- root/root 57515 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2-eukns.cm -rw-r--r-- root/root 45507 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2.cm -rw-r--r-- root/root 57515 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNA2ns.cm -rw-r--r-- root/root 20299 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-arch-3h-nc.cm -rw-r--r-- root/root 12959 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-arch-5h-nc.cm -rw-r--r-- root/root 37296 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-arch-c.cm -rw-r--r-- root/root 33396 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-arch-ns-c.cm -rw-r--r-- root/root 36924 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-bact-c.cm -rw-r--r-- root/root 33400 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-bact-ns-c.cm -rw-r--r-- root/root 38945 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-c.cm -rw-r--r-- root/root 36615 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-euk-c.cm -rw-r--r-- root/root 32761 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-euk-ns-c.cm -rw-r--r-- root/root 35830 2016-12-14 07:35 ./usr/share/tRNAscan-SE/TRNAinf-ns-c.cm -rw-r--r-- root/root 143 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.cilnuc -rw-r--r-- root/root 143 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.echdmito -rw-r--r-- root/root 146 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.invmito -rw-r--r-- root/root 144 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.othmito -rw-r--r-- root/root 144 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.vertmito -rw-r--r-- root/root 139 2016-12-14 07:35 ./usr/share/tRNAscan-SE/gcode.ystmito trnascan-se_1.3.1-1_amd64.deb ----------------------------- new debian package, version 2.0. size 140142 bytes: control archive=1306 bytes. 1186 bytes, 21 lines control 1029 bytes, 16 lines md5sums Package: trnascan-se Version: 1.3.1-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 573 Depends: libc6 (>= 2.14), perl:any, trnascan-se-common (= 1.3.1-1) Suggests: infernal (>= 1.0) Section: non-free/science Priority: optional Homepage: http://lowelab.ucsc.edu/tRNAscan-SE Description: detection of transfer RNA genes in genomic sequence tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes. drwxr-xr-x root/root 0 2016-12-14 07:35 ./ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/bin/ -rwxr-xr-x root/root 180904 2016-12-14 07:35 ./usr/bin/covels-SE -rwxr-xr-x root/root 180744 2016-12-14 07:35 ./usr/bin/coves-SE -rwxr-xr-x root/root 100072 2016-12-14 07:35 ./usr/bin/eufindtRNA -rwxr-xr-x root/root 44859 2016-12-14 07:35 ./usr/bin/tRNAscan-SE -rwxr-xr-x root/root 23136 2016-12-14 07:35 ./usr/bin/trnascan-1.4 drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/doc/trnascan-se/ -rw-r--r-- root/root 16387 2008-06-04 10:30 ./usr/share/doc/trnascan-se/MANUAL.gz -rw-r--r-- root/root 2235 2012-01-15 07:17 ./usr/share/doc/trnascan-se/README.gz -rw-r--r-- root/root 159 2016-12-14 07:35 ./usr/share/doc/trnascan-se/changelog.Debian.gz -rw-r--r-- root/root 2324 2016-12-14 07:21 ./usr/share/doc/trnascan-se/copyright drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/man/ drwxr-xr-x root/root 0 2016-12-14 07:35 ./usr/share/man/man1/ -rw-r--r-- root/root 801 2016-12-14 07:35 ./usr/share/man/man1/covels-SE.1.gz -rw-r--r-- root/root 801 2016-12-14 07:35 ./usr/share/man/man1/covels.1.gz -rw-r--r-- root/root 352 2016-12-14 07:35 ./usr/share/man/man1/coves-SE.1.gz -rw-r--r-- root/root 352 2016-12-14 07:35 ./usr/share/man/man1/coves.1.gz -rw-r--r-- root/root 322 2016-12-14 07:35 ./usr/share/man/man1/eufindtRNA.1.gz -rw-r--r-- root/root 7876 2016-12-14 07:35 ./usr/share/man/man1/tRNAscan-SE.1.gz -rw-r--r-- root/root 193 2016-12-14 07:35 ./usr/share/man/man1/trnascan-1.4.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 13248 Build-Time: 15 Distribution: artful-proposed Host Architecture: amd64 Install-Time: 8 Job: trnascan-se_1.3.1-1.dsc Machine Architecture: amd64 Package: trnascan-se Package-Time: 24 Source-Version: 1.3.1-1 Space: 13248 Status: successful Version: 1.3.1-1 -------------------------------------------------------------------------------- Finished at 20170430-0222 Build needed 00:00:24, 13248k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12501013'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12501013/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12501013'] Unmounting chroot for build PACKAGEBUILD-12501013... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12501013'] Removing build PACKAGEBUILD-12501013