RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.24-32-xen #1 SMP Thu Jul 12 14:30:40 UTC 2012 x86_64 Buildd toolchain package versions: launchpad-buildd_113~0.IS.08.04 python-lpbuildd_113~0.IS.08.04 bzr-builder_0.7.2+bzr156-0ubuntu1~1.IS.8.04 bzr_2.4.0-0ubuntu2~11.IS.8.04. Syncing the system clock with the buildd NTP service... 26 Aug 00:15:50 ntpdate[3414]: step time server 10.211.37.1 offset -158965.665823 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897', '/home/buildd/filecache-default/c021ff3d3373fb2201b3008c0ece6808393ff246'] Uncompressing the tarball... Unpacking chroot for build d3ffa0b946802d3b9c76683b2a5490ae16f73897 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897'] Mounting chroot for build d3ffa0b946802d3b9c76683b2a5490ae16f73897 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897', 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main', 'deb http://ftpmaster.internal/ubuntu precise main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu precise-updates main restricted universe multiverse'] Overriding sources.list in build-d3ffa0b946802d3b9c76683b2a5490ae16f73897 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897', 'amd64'] Updating debian chroot for build d3ffa0b946802d3b9c76683b2a5490ae16f73897 Ign http://ftpmaster.internal precise InRelease Ign http://ftpmaster.internal precise-security InRelease Ign http://ftpmaster.internal precise-updates InRelease Get:1 http://ftpmaster.internal precise Release.gpg [198 B] Get:2 http://ftpmaster.internal precise-security Release.gpg [198 B] Get:3 http://ftpmaster.internal precise-updates Release.gpg [198 B] Get:4 http://ftpmaster.internal precise Release [49.6 kB] Get:5 http://ftpmaster.internal precise-security Release [49.6 kB] Get:6 http://ftpmaster.internal precise-updates Release [49.6 kB] Get:7 http://ftpmaster.internal precise/main amd64 Packages [1273 kB] Ign http://ppa.launchpad.net precise InRelease Get:8 http://ppa.launchpad.net precise Release.gpg [316 B] Get:9 http://ppa.launchpad.net precise Release [11.9 kB] Ign http://ppa.launchpad.net precise Release Get:10 http://ppa.launchpad.net precise/main amd64 Packages [12.9 kB] Ign http://ppa.launchpad.net precise/main TranslationIndex Ign http://ppa.launchpad.net precise/main Translation-en Get:11 http://ftpmaster.internal precise/restricted amd64 Packages [8452 B] Get:12 http://ftpmaster.internal precise/universe amd64 Packages [4786 kB] Get:13 http://ftpmaster.internal precise/multiverse amd64 Packages [119 kB] Get:14 http://ftpmaster.internal precise/main TranslationIndex [3706 B] Get:15 http://ftpmaster.internal precise/multiverse TranslationIndex [2676 B] Get:16 http://ftpmaster.internal precise/restricted TranslationIndex [2596 B] Get:17 http://ftpmaster.internal precise/universe TranslationIndex [2922 B] Get:18 http://ftpmaster.internal precise-security/main amd64 Packages [157 kB] Get:19 http://ftpmaster.internal precise-security/restricted amd64 Packages [3969 B] Get:20 http://ftpmaster.internal precise-security/universe amd64 Packages [41.2 kB] Get:21 http://ftpmaster.internal precise-security/multiverse amd64 Packages [2180 B] Get:22 http://ftpmaster.internal precise-security/main TranslationIndex [73 B] Get:23 http://ftpmaster.internal precise-security/multiverse TranslationIndex [71 B] Get:24 http://ftpmaster.internal precise-security/restricted TranslationIndex [71 B] Get:25 http://ftpmaster.internal precise-security/universe TranslationIndex [73 B] Get:26 http://ftpmaster.internal precise-updates/main amd64 Packages [374 kB] Get:27 http://ftpmaster.internal precise-updates/restricted amd64 Packages [6755 B] Get:28 http://ftpmaster.internal precise-updates/universe amd64 Packages [126 kB] Get:29 http://ftpmaster.internal precise-updates/multiverse amd64 Packages [8677 B] Get:30 http://ftpmaster.internal precise-updates/main TranslationIndex [3564 B] Get:31 http://ftpmaster.internal precise-updates/multiverse TranslationIndex [2605 B] Get:32 http://ftpmaster.internal precise-updates/restricted TranslationIndex [2461 B] Get:33 http://ftpmaster.internal precise-updates/universe TranslationIndex [2850 B] Get:34 http://ftpmaster.internal precise/main Translation-en [726 kB] Get:35 http://ftpmaster.internal precise/multiverse Translation-en [93.4 kB] Get:36 http://ftpmaster.internal precise/restricted Translation-en [2395 B] Get:37 http://ftpmaster.internal precise/universe Translation-en [3341 kB] Get:38 http://ftpmaster.internal precise-security/main Translation-en [74.6 kB] Get:39 http://ftpmaster.internal precise-security/multiverse Translation-en [995 B] Get:40 http://ftpmaster.internal precise-security/restricted Translation-en [978 B] Get:41 http://ftpmaster.internal precise-security/universe Translation-en [25.6 kB] Get:42 http://ftpmaster.internal precise-updates/main Translation-en [181 kB] Get:43 http://ftpmaster.internal precise-updates/multiverse Translation-en [5414 B] Get:44 http://ftpmaster.internal precise-updates/restricted Translation-en [1484 B] Get:45 http://ftpmaster.internal precise-updates/universe Translation-en [75.6 kB] Fetched 11.6 MB in 6s (1813 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https base-files initscripts libapt-pkg4.12 libgcrypt11 libglib2.0-0 libgnutls26 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libsasl2-2 libsqlite3-0 libssl1.0.0 libtasn1-3 libudev0 linux-libc-dev openssl perl perl-base perl-modules python2.7-minimal sysv-rc sysvinit-utils tzdata udev upstart 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 20.0 MB of archives. After this operation, 37.9 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files perl perl-base perl-modules libapt-pkg4.12 apt libssl1.0.0 libsqlite3-0 libglib2.0-0 libudev0 libgcrypt11 libtasn1-3 libgnutls26 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libsasl2-2 libldap-2.4-2 python2.7-minimal tzdata sysvinit-utils sysv-rc initscripts upstart udev apt-transport-https linux-libc-dev openssl Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise-updates/main base-files amd64 6.5ubuntu6.2 [69.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-updates/main perl amd64 5.14.2-6ubuntu2.1 [4416 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-base amd64 5.14.2-6ubuntu2.1 [1498 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise-updates/main perl-modules all 5.14.2-6ubuntu2.1 [3396 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise-security/main libapt-pkg4.12 amd64 0.8.16~exp12ubuntu10.2 [932 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise-security/main apt amd64 0.8.16~exp12ubuntu10.2 [1092 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise-security/main libssl1.0.0 amd64 1.0.1-4ubuntu5.3 [1011 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise-updates/main libsqlite3-0 amd64 3.7.9-2ubuntu1.1 [349 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise-updates/main libglib2.0-0 amd64 2.32.3-0ubuntu1 [1199 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise-updates/main libudev0 amd64 175-0ubuntu9.1 [30.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise-updates/main libgcrypt11 amd64 1.5.0-3ubuntu0.1 [280 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise-security/main libtasn1-3 amd64 2.10-1ubuntu1.1 [43.3 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise-updates/main libgnutls26 amd64 2.12.14-5ubuntu3.1 [459 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise-security/main libk5crypto3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [80.1 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise-security/main libgssapi-krb5-2 amd64 1.10+dfsg~beta1-2ubuntu0.3 [118 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5-3 amd64 1.10+dfsg~beta1-2ubuntu0.3 [355 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-security/main libkrb5support0 amd64 1.10+dfsg~beta1-2ubuntu0.3 [23.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ precise-updates/main libsasl2-2 amd64 2.1.25.dfsg1-3ubuntu0.1 [69.1 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise-updates/main libldap-2.4-2 amd64 2.4.28-1.1ubuntu4.1 [186 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise-updates/main python2.7-minimal amd64 2.7.3-0ubuntu3.1 [1741 kB] Get:21 http://ftpmaster.internal/ubuntu/ precise-updates/main tzdata all 2012e-0ubuntu0.12.04 [438 kB] Get:22 http://ftpmaster.internal/ubuntu/ precise-updates/main sysvinit-utils amd64 2.88dsf-13.10ubuntu11.1 [60.2 kB] Get:23 http://ftpmaster.internal/ubuntu/ precise-updates/main sysv-rc all 2.88dsf-13.10ubuntu11.1 [44.6 kB] Get:24 http://ftpmaster.internal/ubuntu/ precise-updates/main initscripts amd64 2.88dsf-13.10ubuntu11.1 [28.1 kB] Get:25 http://ftpmaster.internal/ubuntu/ precise-updates/main upstart amd64 1.5-0ubuntu7 [311 kB] Get:26 http://ftpmaster.internal/ubuntu/ precise-updates/main udev amd64 175-0ubuntu9.1 [323 kB] Get:27 http://ftpmaster.internal/ubuntu/ precise-security/main apt-transport-https amd64 0.8.16~exp12ubuntu10.2 [16.3 kB] Get:28 http://ftpmaster.internal/ubuntu/ precise-security/main linux-libc-dev amd64 3.2.0-29.46 [871 kB] Get:29 http://ftpmaster.internal/ubuntu/ precise-security/main openssl amd64 1.0.1-4ubuntu5.3 [523 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.0 MB in 0s (32.1 MB/s) (Reading database ... 12243 files and directories currently installed.) Preparing to replace base-files 6.5ubuntu6 (using .../base-files_6.5ubuntu6.2_amd64.deb) ... Unpacking replacement base-files ... Setting up base-files (6.5ubuntu6.2) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12243 files and directories currently installed.) Preparing to replace perl 5.14.2-6ubuntu2 (using .../perl_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-6ubuntu2 (using .../perl-base_5.14.2-6ubuntu2.1_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-6ubuntu2.1) ... (Reading database ... 12243 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-6ubuntu2 (using .../perl-modules_5.14.2-6ubuntu2.1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace libapt-pkg4.12 0.8.16~exp12ubuntu10 (using .../libapt-pkg4.12_0.8.16~exp12ubuntu10.2_amd64.deb) ... Unpacking replacement libapt-pkg4.12 ... Setting up libapt-pkg4.12 (0.8.16~exp12ubuntu10.2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12243 files and directories currently installed.) Preparing to replace apt 0.8.16~exp12ubuntu10 (using .../apt_0.8.16~exp12ubuntu10.2_amd64.deb) ... Unpacking replacement apt ... Setting up apt (0.8.16~exp12ubuntu10.2) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: Total number processed: 2 gpg: unchanged: 2 (Reading database ... 12243 files and directories currently installed.) Preparing to replace libssl1.0.0 1.0.1-4ubuntu3 (using .../libssl1.0.0_1.0.1-4ubuntu5.3_amd64.deb) ... Unpacking replacement libssl1.0.0 ... Setting up libssl1.0.0 (1.0.1-4ubuntu5.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 12243 files and directories currently installed.) Preparing to replace libsqlite3-0 3.7.9-2ubuntu1 (using .../libsqlite3-0_3.7.9-2ubuntu1.1_amd64.deb) ... Unpacking replacement libsqlite3-0 ... Preparing to replace libglib2.0-0 2.32.1-0ubuntu2 (using .../libglib2.0-0_2.32.3-0ubuntu1_amd64.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libudev0 175-0ubuntu9 (using .../libudev0_175-0ubuntu9.1_amd64.deb) ... Unpacking replacement libudev0 ... Preparing to replace libgcrypt11 1.5.0-3 (using .../libgcrypt11_1.5.0-3ubuntu0.1_amd64.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libtasn1-3 2.10-1ubuntu1 (using .../libtasn1-3_2.10-1ubuntu1.1_amd64.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.12.14-5ubuntu3 (using .../libgnutls26_2.12.14-5ubuntu3.1_amd64.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libk5crypto3 1.10+dfsg~beta1-2 (using .../libk5crypto3_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.10+dfsg~beta1-2 (using .../libgssapi-krb5-2_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.10+dfsg~beta1-2 (using .../libkrb5-3_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.10+dfsg~beta1-2 (using .../libkrb5support0_1.10+dfsg~beta1-2ubuntu0.3_amd64.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libsasl2-2 2.1.25.dfsg1-3 (using .../libsasl2-2_2.1.25.dfsg1-3ubuntu0.1_amd64.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libldap-2.4-2 2.4.28-1.1ubuntu4 (using .../libldap-2.4-2_2.4.28-1.1ubuntu4.1_amd64.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu3.1_amd64.deb) ... Unpacking replacement python2.7-minimal ... Setting up python2.7-minimal (2.7.3-0ubuntu3.1) ... (Reading database ... 12243 files and directories currently installed.) Preparing to replace tzdata 2012b-1 (using .../tzdata_2012e-0ubuntu0.12.04_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2012e-0ubuntu0.12.04) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Aug 24 04:09:17 UTC 2012. Universal Time is now: Fri Aug 24 04:09:17 UTC 2012. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12243 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu11.1_amd64.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu11 (using .../sysv-rc_2.88dsf-13.10ubuntu11.1_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.88dsf-13.10ubuntu11 (using .../initscripts_2.88dsf-13.10ubuntu11.1_amd64.deb) ... Unpacking replacement initscripts ... Preparing to replace upstart 1.5-0ubuntu5 (using .../upstart_1.5-0ubuntu7_amd64.deb) ... Unpacking replacement upstart ... Preparing to replace udev 175-0ubuntu9 (using .../udev_175-0ubuntu9.1_amd64.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace apt-transport-https 0.8.16~exp12ubuntu10 (using .../apt-transport-https_0.8.16~exp12ubuntu10.2_amd64.deb) ... Unpacking replacement apt-transport-https ... Preparing to replace linux-libc-dev 3.2.0-23.36 (using .../linux-libc-dev_3.2.0-29.46_amd64.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace openssl 1.0.1-4ubuntu3 (using .../openssl_1.0.1-4ubuntu5.3_amd64.deb) ... Unpacking replacement openssl ... Setting up libsqlite3-0 (3.7.9-2ubuntu1.1) ... Setting up libglib2.0-0 (2.32.3-0ubuntu1) ... No schema files found: doing nothing. Setting up libudev0 (175-0ubuntu9.1) ... Setting up libgcrypt11 (1.5.0-3ubuntu0.1) ... Setting up libtasn1-3 (2.10-1ubuntu1.1) ... Setting up libgnutls26 (2.12.14-5ubuntu3.1) ... Setting up libkrb5support0 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libk5crypto3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libkrb5-3 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libgssapi-krb5-2 (1.10+dfsg~beta1-2ubuntu0.3) ... Setting up libsasl2-2 (2.1.25.dfsg1-3ubuntu0.1) ... Setting up libldap-2.4-2 (2.4.28-1.1ubuntu4.1) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu11.1) ... Setting up sysv-rc (2.88dsf-13.10ubuntu11.1) ... Setting up apt-transport-https (0.8.16~exp12ubuntu10.2) ... Setting up linux-libc-dev (3.2.0-29.46) ... Setting up openssl (1.0.1-4ubuntu5.3) ... Setting up perl-modules (5.14.2-6ubuntu2.1) ... Setting up upstart (1.5-0ubuntu7) ... Installing new version of config file /etc/logrotate.d/upstart ... Setting up udev (175-0ubuntu9.1) ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up perl (5.14.2-6ubuntu2.1) ... Setting up initscripts (2.88dsf-13.10ubuntu11.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897', 'amd64', 'precise', '--nolog', '--batch', '--archive=ubuntu', '--dist=precise', '--purpose=PPA', '--architecture=amd64', '--comp=main', 't-coffee_9.03.r1318-1ubuntu2.dsc'] Initiating build d3ffa0b946802d3b9c76683b2a5490ae16f73897 with 2 jobs across 2 processor cores. Automatic build of t-coffee_9.03.r1318-1ubuntu2 on pluot by sbuild/amd64 1.170.5 Build started at 20120824-0409 ****************************************************************************** t-coffee_9.03.r1318-1ubuntu2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), gfortran Checking for already installed source dependencies... debhelper: missing gfortran: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper gfortran Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor file gettext gettext-base gfortran-4.6 groff-base html2text intltool-debian libcroco3 libgettextpo0 libgfortran3 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc gfortran-multilib gfortran-doc gfortran-4.6-multilib gfortran-4.6-doc libgfortran3-dbg groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor file gettext gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian libcroco3 libgettextpo0 libgfortran3 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 11.8 MB of archives. After this operation, 34.4 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 libgfortran3 libmagic1 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf dh-apparmor debhelper gfortran-4.6 gfortran Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ precise/main libpipeline1 amd64 1.2.1-1 [26.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ precise-security/main libxml2 amd64 2.7.8.dfsg-5.1ubuntu4.1 [673 kB] Get:3 http://ftpmaster.internal/ubuntu/ precise/main libcroco3 amd64 0.6.5-1 [99.3 kB] Get:4 http://ftpmaster.internal/ubuntu/ precise/main libunistring0 amd64 0.9.3-5 [427 kB] Get:5 http://ftpmaster.internal/ubuntu/ precise/main libgettextpo0 amd64 0.18.1.1-5ubuntu3 [120 kB] Get:6 http://ftpmaster.internal/ubuntu/ precise/main libgfortran3 amd64 4.6.3-1ubuntu5 [357 kB] Get:7 http://ftpmaster.internal/ubuntu/ precise/main libmagic1 amd64 5.09-2 [217 kB] Get:8 http://ftpmaster.internal/ubuntu/ precise/main file amd64 5.09-2 [19.7 kB] Get:9 http://ftpmaster.internal/ubuntu/ precise/main bsdmainutils amd64 8.2.3ubuntu1 [200 kB] Get:10 http://ftpmaster.internal/ubuntu/ precise/main gettext-base amd64 0.18.1.1-5ubuntu3 [80.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ precise/main groff-base amd64 1.21-7 [1046 kB] Get:12 http://ftpmaster.internal/ubuntu/ precise/main man-db amd64 2.6.1-2 [756 kB] Get:13 http://ftpmaster.internal/ubuntu/ precise/main html2text amd64 1.3.2a-15 [104 kB] Get:14 http://ftpmaster.internal/ubuntu/ precise/main gettext amd64 0.18.1.1-5ubuntu3 [1188 kB] Get:15 http://ftpmaster.internal/ubuntu/ precise/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ precise/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:17 http://ftpmaster.internal/ubuntu/ precise-security/main dh-apparmor all 2.7.102-0ubuntu3.1 [9546 B] Get:18 http://ftpmaster.internal/ubuntu/ precise/main debhelper all 9.20120115ubuntu3 [616 kB] Get:19 http://ftpmaster.internal/ubuntu/ precise/main gfortran-4.6 amd64 4.6.3-1ubuntu5 [5579 kB] Get:20 http://ftpmaster.internal/ubuntu/ precise/main gfortran amd64 4:4.6.3-1ubuntu5 [1206 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.8 MB in 0s (21.6 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 12245 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4.1_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.6.3-1ubuntu5_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5ubuntu3_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2ubuntu1_all.deb) ... Selecting previously unselected package dh-apparmor. Unpacking dh-apparmor (from .../dh-apparmor_2.7.102-0ubuntu3.1_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120115ubuntu3_all.deb) ... Selecting previously unselected package gfortran-4.6. Unpacking gfortran-4.6 (from .../gfortran-4.6_4.6.3-1ubuntu5_amd64.deb) ... Selecting previously unselected package gfortran. Unpacking gfortran (from .../gfortran_4%3a4.6.3-1ubuntu5_amd64.deb) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4.1) ... Setting up libcroco3 (0.6.5-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up libgfortran3 (4.6.3-1ubuntu5) ... Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up bsdmainutils (8.2.3ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3.1) ... Setting up debhelper (9.20120115ubuntu3) ... Setting up gfortran-4.6 (4.6.3-1ubuntu5) ... Setting up gfortran (4:4.6.3-1ubuntu5) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu10 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu7 gcc-4.6_4.6.3-1ubuntu5 g++-4.6_4.6.3-1ubuntu5 binutils_2.22-6ubuntu1 libstdc++6-4.6-dev_4.6.3-1ubuntu5 libstdc++6_4.6.3-1ubuntu5 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Aug 22 16:40:45 2012 UTC using DSA key ID 113960C5 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./t-coffee_9.03.r1318-1ubuntu2.dsc dpkg-source: info: extracting t-coffee in t-coffee-9.03.r1318 dpkg-source: info: unpacking t-coffee_9.03.r1318.orig.tar.gz dpkg-source: info: unpacking t-coffee_9.03.r1318-1ubuntu2.debian.tar.gz dpkg-source: info: applying probconsrna.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2 dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro dpkg-buildpackage: source package t-coffee dpkg-buildpackage: source version 9.03.r1318-1ubuntu2 dpkg-source --before-build t-coffee-9.03.r1318 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source dh_testdir -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/t-coffee-9.03.r1318' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign chmod 644 example/* make[1]: Leaving directory `/build/buildd/t-coffee-9.03.r1318' dh_clean -O--sourcedirectory=t_coffee_source debian/rules build dh build --sourcedirectory=t_coffee_source dh_testdir -O--sourcedirectory=t_coffee_source dh_auto_configure -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/t-coffee-9.03.r1318' dh_auto_build -- -i USER_BIN=../bin/ FCC="gfortran -g -O2" all make[2]: Entering directory `/build/buildd/t-coffee-9.03.r1318/t_coffee_source' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_constraints_list.o util_constraints_list.c util_constraints_list.c: In function 'fork_read_n_constraint_list': util_constraints_list.c:2163:4: warning: too many arguments for format [-Wformat-extra-args] util_constraints_list.c: In function 'read_constraint_list_file': util_constraints_list.c:2743:5: warning: too many arguments for format [-Wformat-extra-args] util_constraints_list.c: In function 'nfork_relax_constraint_list_4gp': util_constraints_list.c:3670:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'read_seq_in_list': util_constraints_list.c:2802:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2807:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2838:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2863:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'read_cpu_in_list': util_constraints_list.c:2510:20: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'method_file2TC_method': util_constraints_list.c:1167:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'method_file_tag2value': util_constraints_list.c:1125:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'submit_lib_job': util_constraints_list.c:555:12: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:558:12: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_job_handling.o util_job_handling.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dps.o util_dps.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_domain_constraints_list.o util_domain_constraints_list.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_analyse_constraints_list.o util_analyse_constraints_list.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_aln_analyze.o util_aln_analyze.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o aln_convertion_util.o aln_convertion_util.c aln_convertion_util.c: In function 'extract_aln3': aln_convertion_util.c:6746:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] aln_convertion_util.c:6765:31: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] aln_convertion_util.c:6769:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_declare.o util_declare.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o hsearch.o hsearch.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o random.o random.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_make_tree.o util_make_tree.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util.o util.c util.c: In function 'check_for_update': util.c:7054:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_file_block_pattern': util.c:6937:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c:6967:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'set_fp_id': util.c:6701:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_parameter': util.c:6681:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'count_strings_in_file': util.c:5017:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'perl_strstr': util.c:1871:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'input_array_int': util.c:1215:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1219:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1222:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1223:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'quantile': util.c:828:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_number_list_in_file': util.c:769:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'bsearch_file': util.c:348:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'hsort_file': util.c:209:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:214:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:217:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:234:15: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:239:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o reformat_struc.o reformat_struc.c reformat_struc.c: In function 'simple_read_ca_trace': reformat_struc.c:299:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:301:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:307:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:334:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:336:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:344:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o reformat.o reformat.c reformat.c: In function 'modify_data': reformat.c:10527:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10532:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10765:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10864:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10865:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10872:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10879:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10969:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11074:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11608:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11608:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11615:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11616:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11617:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11618:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11619:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11620:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11643:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11767:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11768:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11772:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12291:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12292:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12293:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12294:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12295:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c: In function 'read_pavie_matrix': reformat.c:12898:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'read_blast_matrix': reformat.c:12737:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12747:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12760:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12787:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'similarities_file2aln': reformat.c:5797:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'output_maln_pval': reformat.c:5632:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'read_gotoh_aln': reformat.c:5412:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:5434:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_amps_seq_name': reformat.c:5363:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'fscanf_seq_name': reformat.c:5010:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_swissprot_sequence': reformat.c:4972:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:4991:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_dialign_sequence': reformat.c:3811:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_sequence_dali': reformat.c:3736:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_struc_gor': reformat.c:3673:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3694:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3699:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'read_rna_struc_number': reformat.c:3473:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3476:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_amps_sd_scores': reformat.c:3165:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3172:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3181:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3187:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3189:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3200:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'format_is_msf': reformat.c:1890:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_pdb_id': reformat.c:1454:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'is_pdb_name': reformat.c:1416:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o aln_compare.o aln_compare.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o io_func.o io_func.c io_func.c: In function 'get_rgb_values': io_func.c:625:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] io_func.c: In function 'read_matrice': io_func.c:428:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o pb_util_read_sequence.o pb_util_read_sequence.c pb_util_read_sequence.c: In function 'get_clustal_seq': pb_util_read_sequence.c:118:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:123:30: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c: In function 'get_msf_seq': pb_util_read_sequence.c:82:30: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c: In function 'get_seq': pb_util_read_sequence.c:157:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:167:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:187:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:196:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:223:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:254:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o pb_util_read_seq_util.o pb_util_read_seq_util.c pb_util_read_seq_util.c: In function 'do_system': pb_util_read_seq_util.c:302:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getint': pb_util_read_seq_util.c:280:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getreal': pb_util_read_seq_util.c:255:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getstr': pb_util_read_seq_util.c:244:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o tree_util.o tree_util.c tree_util.c: In function 'tree_scan': tree_util.c:814:2: warning: too many arguments for format [-Wformat-extra-args] tree_util.c: In function 'create_tree': tree_util.c:2780:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] tree_util.c:2788:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_graph_maln.o util_graph_maln.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_clean_maln.o util_dp_clean_maln.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_ssec_pwaln.o util_dp_ssec_pwaln.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_sim.o util_dp_sim.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_mm_nw.o util_dp_mm_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_gotoh_nw.o util_dp_gotoh_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_suboptimal_nw.o util_dp_suboptimal_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_cdna_fasta_nw.o util_dp_cdna_fasta_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_generic_fasta_nw.o util_dp_generic_fasta_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_fasta_nw.o util_dp_fasta_nw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_fasta_sw.o util_dp_fasta_sw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_gotoh_sw.o util_dp_gotoh_sw.c util_dp_gotoh_sw.c: In function 'gotoh_pair_wise_sw': util_dp_gotoh_sw.c:365:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_est.o util_dp_est.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_domain_dp_drivers.o util_domain_dp_drivers.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_dp_drivers.o util_dp_drivers.c util_dp_drivers.c: In function 'rna_pair': util_dp_drivers.c:1735:6: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'sap_pair': util_dp_drivers.c:1560:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1611:10: warning: ignoring return value of 'getcwd', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1612:9: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1621:9: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'lsqman_pair': util_dp_drivers.c:1488:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'thread_pair': util_dp_drivers.c:1413:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'pdb_pair': util_dp_drivers.c:1274:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'pdbid_pair': util_dp_drivers.c:1214:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'profile_pair': util_dp_drivers.c:1119:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'hh_pair': util_dp_drivers.c:1011:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1065:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'align_pdb_pair': util_dp_drivers.c:970:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'align_pdb_pair_2': util_dp_drivers.c:942:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o util_domain_dp.o util_domain_dp.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o CUSTOM_evaluate_for_struc.o CUSTOM_evaluate_for_struc.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o evaluate_for_struc.o evaluate_for_struc.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o evaluate_for_domain.o evaluate_for_domain.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o evaluate_dirichlet.o evaluate_dirichlet.c evaluate_dirichlet.c: In function 'read_dirichlet': evaluate_dirichlet.c:291:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:293:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:297:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:300:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o evaluate.o evaluate.c evaluate.c: In function 'initialise_aa_physico_chemical_property_table': evaluate.c:4932:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c: In function 'fork_triplet_coffee_evaluate_output': evaluate.c:750:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c:755:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c:760:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o showpair.o showpair.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o fsa_dp.o fsa_dp.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o pavie_dp.o pavie_dp.c pavie_dp.c: In function 'pavie_seq2pavie_msa': pavie_dp.c:1339:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c: In function 'output_pavie_mat_list': pavie_dp.c:1053:15: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c:1055:14: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c: In function 'pavie_seq2pavie_aln': pavie_dp.c:101:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o dev1.o dev1.c dev1.c: In function 'aln2hitMat': dev1.c:63:2: warning: too many arguments for format [-Wformat-extra-args] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o dev2.o dev2.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o dev3.o dev3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o dev4.o dev4.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o fastal.o fastal.c fastal.c: In function 'edit2alignment': fastal.c:3567:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3569:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3571:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3573:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3635:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'edit_seq2aligned_seq': fastal.c:3494:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'profile_file2profile': fastal.c:3315:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3318:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3321:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3323:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3325:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3344:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'file_pos2profile': fastal.c:3193:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blastz_diagonal': fastal.c:2251:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blat_diagonal': fastal.c:2104:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blast_diagonal': fastal.c:1913:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1918:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1919:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1920:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1965:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1969:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1970:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1971:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o parttree.o parttree.c parttree.c: In function 'euclidean_dist_half': parttree.c:925:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:936:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'euclidean_dist': parttree.c:865:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:877:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:880:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:886:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'get_table': parttree.c:822:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:833:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'make_distance_matrix_sim': parttree.c:669:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:675:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o tree.o tree.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o diagonal.o diagonal.c diagonal.c: In function 'seq_pair2blast_diagonal2': diagonal.c:408:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:413:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:414:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:415:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o fastal_opt_parsing.o fastal_opt_parsing.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o scoring.o scoring.c scoring.c: In function 'agreement_score': scoring.c:560:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:561:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:562:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'make_ref_alignment': scoring.c:464:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:478:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'compute_ref_alignments': scoring.c:359:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:373:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'calculate_sum_of_pairs_score_affine': scoring.c:50:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:52:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:56:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o iteration.o iteration.c iteration.c: In function 'edit2seq_pattern': iteration.c:533:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:535:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:537:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:539:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'write_iterated_aln': iteration.c:471:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:474:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:505:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'iterate': iteration.c:280:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:405:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'split_set': iteration.c:155:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o Stack.o Stack.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o Vector.o Vector.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o classes.o classes.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o km_util.o km_util.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o kmeans.o kmeans.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o km_coffee.o km_coffee.c km_coffee.c: In function 'km_coffee_align3': km_coffee.c:222:7: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o t_coffee.o t_coffee.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm gfortran -g -O2 TMalign.f -o TMalign make[2]: Leaving directory `/build/buildd/t-coffee-9.03.r1318/t_coffee_source' make[1]: Leaving directory `/build/buildd/t-coffee-9.03.r1318' dh_auto_test -O--sourcedirectory=t_coffee_source /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_installdirs -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_installdocs -a -O--sourcedirectory=t_coffee_source dh_installchangelogs -a -O--sourcedirectory=t_coffee_source dh_installexamples -a -O--sourcedirectory=t_coffee_source dh_installman -a -O--sourcedirectory=t_coffee_source dh_installcatalogs -a -O--sourcedirectory=t_coffee_source dh_installcron -a -O--sourcedirectory=t_coffee_source dh_installdebconf -a -O--sourcedirectory=t_coffee_source dh_installemacsen -a -O--sourcedirectory=t_coffee_source dh_installifupdown -a -O--sourcedirectory=t_coffee_source dh_installinfo -a -O--sourcedirectory=t_coffee_source dh_installinit -a -O--sourcedirectory=t_coffee_source dh_installmenu -a -O--sourcedirectory=t_coffee_source dh_installmime -a -O--sourcedirectory=t_coffee_source dh_installmodules -a -O--sourcedirectory=t_coffee_source dh_installlogcheck -a -O--sourcedirectory=t_coffee_source dh_installlogrotate -a -O--sourcedirectory=t_coffee_source dh_installpam -a -O--sourcedirectory=t_coffee_source dh_installppp -a -O--sourcedirectory=t_coffee_source dh_installudev -a -O--sourcedirectory=t_coffee_source dh_installwm -a -O--sourcedirectory=t_coffee_source dh_installxfonts -a -O--sourcedirectory=t_coffee_source dh_installgsettings -a -O--sourcedirectory=t_coffee_source dh_bugfiles -a -O--sourcedirectory=t_coffee_source dh_ucf -a -O--sourcedirectory=t_coffee_source dh_lintian -a -O--sourcedirectory=t_coffee_source dh_gconf -a -O--sourcedirectory=t_coffee_source dh_icons -a -O--sourcedirectory=t_coffee_source dh_perl -a -O--sourcedirectory=t_coffee_source dh_usrlocal -a -O--sourcedirectory=t_coffee_source dh_link -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/t-coffee-9.03.r1318' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory `/build/buildd/t-coffee-9.03.r1318' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dh_md5sums -a -O--sourcedirectory=t_coffee_source dh_builddeb -a -O--sourcedirectory=t_coffee_source INFO: pkgstriptranslations version 116 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package `t-coffee' in `../t-coffee_9.03.r1318-1ubuntu2_amd64.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../t-coffee_9.03.r1318-1ubuntu2_amd64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build t-coffee-9.03.r1318 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120824-0411 chroot-autobuild/build/buildd/t-coffee_9.03.r1318-1ubuntu2_amd64.deb: new debian package, version 2.0. size 858814 bytes: control archive= 1211 bytes. 1519 bytes, 29 lines control 333 bytes, 5 lines md5sums Package: t-coffee Version: 9.03.r1318-1ubuntu2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1956 Depends: libc6 (>= 2.14) Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align Suggests: boxshade, seaview, t-coffee-examples, dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw, amap-align, proda Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. chroot-autobuild/build/buildd/t-coffee_9.03.r1318-1ubuntu2_amd64.deb: drwxr-xr-x root/root 0 2012-08-24 04:11 ./ drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/ drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/bin/ -rwxr-xr-x root/root 1958184 2012-08-24 04:11 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/share/ drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1630 2012-08-22 15:48 ./usr/share/doc/t-coffee/copyright -rw-r--r-- root/root 2269 2012-08-22 16:33 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1744 2012-08-22 15:48 ./usr/share/doc/t-coffee/README.Debian drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/share/man/ drwxr-xr-x root/root 0 2012-08-24 04:11 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2012-08-24 04:11 ./usr/share/man/man1/t_coffee.1.gz t-coffee_9.03.r1318-1ubuntu2_amd64.changes: Format: 1.8 Date: Wed, 22 Aug 2012 17:33:25 +0100 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: amd64 Version: 9.03.r1318-1ubuntu2 Distribution: precise Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Tim Booth Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Changes: t-coffee (9.03.r1318-1ubuntu2) precise; urgency=low . * Rejigged the rules file to use DH, not CDBS * Avoid compressing files under t-coffee-examples Checksums-Sha1: 36a84cefda5aef9e1c334678348edc35cf809964 858814 t-coffee_9.03.r1318-1ubuntu2_amd64.deb Checksums-Sha256: 2e3731bf3c06067a52ba6d1ab706e39fe7033546bd31b826702f19a391d3b94b 858814 t-coffee_9.03.r1318-1ubuntu2_amd64.deb Files: 793b58f62e5681f6aa3c5bea755a0cca 858814 science optional t-coffee_9.03.r1318-1ubuntu2_amd64.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120824-0411 Build needed 00:01:15, 33440k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897'] Scanning for processes to kill in build /home/buildd/build-d3ffa0b946802d3b9c76683b2a5490ae16f73897/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897'] Unmounting chroot for build d3ffa0b946802d3b9c76683b2a5490ae16f73897... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'd3ffa0b946802d3b9c76683b2a5490ae16f73897'] Removing build d3ffa0b946802d3b9c76683b2a5490ae16f73897