RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux fisher03 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_124~0.IS.08.04 python-lpbuildd_124~0.IS.08.04 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 24 Oct 09:09:40 ntpdate[23975]: adjust time server 10.211.37.1 offset -0.000030 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6487754', '/home/buildd/filecache-default/0ef1c011ee7ed9eb33dd33237ba11b0bf82afae6'] Unpacking chroot for build PACKAGEBUILD-6487754 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6487754'] Mounting chroot for build PACKAGEBUILD-6487754 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6487754', 'deb http://ftpmaster.internal/ubuntu vivid main universe', 'deb http://ftpmaster.internal/ubuntu vivid-security main universe', 'deb http://ftpmaster.internal/ubuntu vivid-updates main universe', 'deb http://ftpmaster.internal/ubuntu vivid-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-6487754 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6487754', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-6487754 Ign http://ftpmaster.internal vivid InRelease Ign http://archive-team.internal vivid InRelease Ign http://ftpmaster.internal vivid-security InRelease Ign http://archive-team.internal vivid Release.gpg Ign http://ftpmaster.internal vivid-updates InRelease Get:1 http://archive-team.internal vivid Release [742 B] Ign http://ftpmaster.internal vivid-proposed InRelease Get:2 http://ftpmaster.internal vivid Release.gpg [933 B] Get:3 http://ftpmaster.internal vivid-security Release.gpg [933 B] Get:4 http://ftpmaster.internal vivid-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal vivid-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal vivid Release [112 kB] Get:7 http://archive-team.internal vivid/main ppc64el Packages Ign http://archive-team.internal vivid/main Translation-en Get:8 http://ftpmaster.internal vivid-security Release [59.7 kB] Get:9 http://ftpmaster.internal vivid-updates Release [59.7 kB] Get:10 http://ftpmaster.internal vivid-proposed Release [59.7 kB] Get:11 http://ftpmaster.internal vivid/main ppc64el Packages [1279 kB] Get:12 http://ftpmaster.internal vivid/universe ppc64el Packages [5884 kB] Get:13 http://ftpmaster.internal vivid/main Translation-en [769 kB] Get:14 http://ftpmaster.internal vivid/universe Translation-en [4267 kB] Get:15 http://ftpmaster.internal vivid-security/main ppc64el Packages [14 B] Get:16 http://ftpmaster.internal vivid-security/universe ppc64el Packages [14 B] Get:17 http://ftpmaster.internal vivid-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal vivid-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal vivid-updates/main ppc64el Packages [14 B] Get:20 http://ftpmaster.internal vivid-updates/universe ppc64el Packages [14 B] Get:21 http://ftpmaster.internal vivid-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal vivid-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal vivid-proposed/main ppc64el Packages [39.6 kB] Get:24 http://ftpmaster.internal vivid-proposed/universe ppc64el Packages [96.7 kB] Get:25 http://ftpmaster.internal vivid-proposed/main Translation-en [27.8 kB] Get:26 http://ftpmaster.internal vivid-proposed/universe Translation-en [109 kB] Fetched 12.8 MB in 13s (919 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils ca-certificates cpp-4.9 g++-4.9 gcc-4.9 gcc-4.9-base grep libacl1 libatomic1 libdb5.3 libgcc-4.9-dev libgcc1 libgmp10 libgomp1 libgssapi-krb5-2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libsasl2-2 libsasl2-modules-db libstdc++-4.9-dev libstdc++6 tzdata 25 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 28.2 MB of archives. After this operation, 81.9 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main base-files ppc64el 7.2ubuntu8 [60.4 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main grep ppc64el 2.20-4 [139 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9-base ppc64el 4.9.1-19ubuntu1 [15.7 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++6 ppc64el 4.9.1-19ubuntu1 [297 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgomp1 ppc64el 4.9.1-19ubuntu1 [36.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libitm1 ppc64el 4.9.1-19ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libatomic1 ppc64el 4.9.1-19ubuntu1 [8234 B] Get:8 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc-4.9-dev ppc64el 4.9.1-19ubuntu1 [266 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid-proposed/main cpp-4.9 ppc64el 4.9.1-19ubuntu1 [4775 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid-proposed/main binutils ppc64el 2.24.90.20141023-1ubuntu1 [2173 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9 ppc64el 4.9.1-19ubuntu1 [5194 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid-proposed/main g++-4.9 ppc64el 4.9.1-19ubuntu1 [12.2 MB] Get:13 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++-4.9-dev ppc64el 4.9.1-19ubuntu1 [1129 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc1 ppc64el 1:4.9.1-19ubuntu1 [29.3 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgmp10 ppc64el 2:6.0.0+dfsg-6 [223 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main libacl1 ppc64el 2.2.52-2 [15.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libdb5.3 ppc64el 5.3.28-6 [633 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgssapi-krb5-2 ppc64el 1.12.1+dfsg-11 [109 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libkrb5-3 ppc64el 1.12.1+dfsg-11 [265 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libkrb5support0 ppc64el 1.12.1+dfsg-11 [29.8 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libk5crypto3 ppc64el 1.12.1+dfsg-11 [101 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsasl2-modules-db ppc64el 2.1.26.dfsg1-12 [14.2 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsasl2-2 ppc64el 2.1.26.dfsg1-12 [48.2 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main tzdata all 2014i-1 [182 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid-proposed/main ca-certificates all 20141019 [192 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.2 MB in 9s (2905 kB/s) (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu8_ppc64el.deb ... Unpacking base-files (7.2ubuntu8) over (7.2ubuntu7) ... Setting up base-files (7.2ubuntu8) ... 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 ... Installing new version of config file /etc/os-release ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../grep_2.20-4_ppc64el.deb ... Unpacking grep (2.20-4) over (2.20-3) ... Setting up grep (2.20-4) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../gcc-4.9-base_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking gcc-4.9-base:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up gcc-4.9-base:ppc64el (4.9.1-19ubuntu1) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libstdc++6:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Setting up libstdc++6:ppc64el (4.9.1-19ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgomp1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgomp1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libitm1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libitm1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libatomic1_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libatomic1:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libgcc-4.9-dev_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgcc-4.9-dev:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../cpp-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking cpp-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../binutils_2.24.90.20141023-1ubuntu1_ppc64el.deb ... Unpacking binutils (2.24.90.20141023-1ubuntu1) over (2.24.90.20141014-0ubuntu3) ... Preparing to unpack .../gcc-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking gcc-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../g++-4.9_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking g++-4.9 (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libstdc++-4.9-dev_4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libstdc++-4.9-dev:ppc64el (4.9.1-19ubuntu1) over (4.9.1-16ubuntu6) ... Preparing to unpack .../libgcc1_1%3a4.9.1-19ubuntu1_ppc64el.deb ... Unpacking libgcc1:ppc64el (1:4.9.1-19ubuntu1) over (1:4.9.1-16ubuntu6) ... Setting up libgcc1:ppc64el (1:4.9.1-19ubuntu1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.0.0+dfsg-6_ppc64el.deb ... Unpacking libgmp10:ppc64el (2:6.0.0+dfsg-6) over (2:6.0.0+dfsg-4build1) ... Preparing to unpack .../libacl1_2.2.52-2_ppc64el.deb ... Unpacking libacl1:ppc64el (2.2.52-2) over (2.2.52-1.1) ... Setting up libacl1:ppc64el (2.2.52-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28-6_ppc64el.deb ... Unpacking libdb5.3:ppc64el (5.3.28-6) over (5.3.28-5) ... Setting up libdb5.3:ppc64el (5.3.28-6) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... (Reading database ... 11386 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libgssapi-krb5-2:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5-3_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libkrb5-3:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5support0_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libk5crypto3_1.12.1+dfsg-11_ppc64el.deb ... Unpacking libk5crypto3:ppc64el (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-12_ppc64el.deb ... Unpacking libsasl2-modules-db:ppc64el (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-12_ppc64el.deb ... Unpacking libsasl2-2:ppc64el (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../tzdata_2014i-1_all.deb ... Unpacking tzdata (2014i-1) over (2014h-2) ... Setting up tzdata (2014i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Oct 24 13:10:14 UTC 2014. Universal Time is now: Fri Oct 24 13:10:14 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11389 files and directories currently installed.) Preparing to unpack .../ca-certificates_20141019_all.deb ... Unpacking ca-certificates (20141019) over (20140325) ... Setting up libgomp1:ppc64el (4.9.1-19ubuntu1) ... Setting up libitm1:ppc64el (4.9.1-19ubuntu1) ... Setting up libatomic1:ppc64el (4.9.1-19ubuntu1) ... Setting up libgcc-4.9-dev:ppc64el (4.9.1-19ubuntu1) ... Setting up libgmp10:ppc64el (2:6.0.0+dfsg-6) ... Setting up cpp-4.9 (4.9.1-19ubuntu1) ... Setting up binutils (2.24.90.20141023-1ubuntu1) ... Setting up gcc-4.9 (4.9.1-19ubuntu1) ... Setting up libstdc++-4.9-dev:ppc64el (4.9.1-19ubuntu1) ... Setting up g++-4.9 (4.9.1-19ubuntu1) ... Setting up libkrb5support0:ppc64el (1.12.1+dfsg-11) ... Setting up libk5crypto3:ppc64el (1.12.1+dfsg-11) ... Setting up libkrb5-3:ppc64el (1.12.1+dfsg-11) ... Setting up libgssapi-krb5-2:ppc64el (1.12.1+dfsg-11) ... Setting up libsasl2-modules-db:ppc64el (2.1.26.dfsg1-12) ... Setting up libsasl2-2:ppc64el (2.1.26.dfsg1-12) ... Setting up ca-certificates (20141019) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for ca-certificates (20141019) ... Updating certificates in /etc/ssl/certs... 10 added, 5 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6487754', 'ppc64el', 'vivid-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=vivid-proposed', '--purpose=PRIMARY', '--architecture=ppc64el', '--comp=universe', 'disulfinder_1.2.11-4.dsc'] Initiating build PACKAGEBUILD-6487754 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-16-generic #36-Ubuntu SMP Tue Mar 4 23:03:28 UTC 2014 ppc64le Automatic build of disulfinder_1.2.11-4 on fisher03 by sbuild/ppc64el 1.170.5 Build started at 20141024-0910 ****************************************************************************** disulfinder_1.2.11-4.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), libboost-dev, libboost-graph-dev, libf2c2-dev Checking for already installed source dependencies... debhelper: missing libboost-dev: missing libboost-graph-dev: missing libf2c2-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper libboost-dev libboost-graph-dev libf2c2-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor file gettext gettext-base groff-base intltool-debian libasprintf0c2 libboost-graph1.55-dev libboost-graph1.55.0 libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-test1.55-dev libboost-test1.55.0 libboost1.55-dev libcroco3 libf2c2 libglib2.0-0 libicu52 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff libboost-doc graphviz libboost1.55-doc libboost-atomic1.55-dev libboost-chrono1.55-dev libboost-context1.55-dev libboost-coroutine1.55-dev libboost-date-time1.55-dev libboost-exception1.55-dev libboost-filesystem1.55-dev libboost-graph-parallel1.55-dev libboost-iostreams1.55-dev libboost-locale1.55-dev libboost-log1.55-dev libboost-math1.55-dev libboost-mpi1.55-dev libboost-mpi-python1.55-dev libboost-program-options1.55-dev libboost-python1.55-dev libboost-random1.55-dev libboost-regex1.55-dev libboost-signals1.55-dev libboost-system1.55-dev libboost-thread1.55-dev libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev libmpfrc++-dev libntl-dev less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor file gettext gettext-base groff-base intltool-debian libasprintf0c2 libboost-dev libboost-graph-dev libboost-graph1.55-dev libboost-graph1.55.0 libboost-regex1.55.0 libboost-serialization1.55-dev libboost-serialization1.55.0 libboost-test1.55-dev libboost-test1.55.0 libboost1.55-dev libcroco3 libf2c2 libf2c2-dev libglib2.0-0 libicu52 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.6 MB of archives. After this operation, 166 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main libmagic1 ppc64el 1:5.19-1ubuntu1.1 [206 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main libasprintf0c2 ppc64el 0.19.2-2ubuntu1 [6352 B] Get:3 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-0 ppc64el 2.42.0-2 [1024 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid/main libpipeline1 ppc64el 1.3.1-1 [23.5 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid/main libxml2 ppc64el 2.9.1+dfsg1-4ubuntu1 [617 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main groff-base ppc64el 1.22.2-8 [1385 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid/main bsdmainutils ppc64el 9.0.5ubuntu1 [173 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid/main man-db ppc64el 2.7.0.2-2 [852 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid/main libicu52 ppc64el 52.1-6 [6902 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid/main libboost-regex1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [249 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [93.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid/main libboost-serialization1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [126 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid/main libboost-test1.55.0 ppc64el 1.55.0+dfsg-1ubuntu3 [168 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid/main libcroco3 ppc64el 0.6.8-3 [77.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/main libunistring0 ppc64el 0.9.3-5ubuntu3 [262 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main file ppc64el 1:5.19-1ubuntu1.1 [20.4 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid/main gettext-base ppc64el 0.19.2-2ubuntu1 [46.5 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid/main gettext ppc64el 0.19.2-2ubuntu1 [866 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main po-debconf all 1.0.16+nmu3 [207 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main dh-apparmor all 2.8.98-0ubuntu2 [11.0 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main debhelper all 9.20141003ubuntu1 [726 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main libboost1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [5801 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main libboost-dev ppc64el 1.55.0.1~ubuntu1 [3222 B] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main libboost-serialization1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [157 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libboost-test1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [226 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph1.55-dev ppc64el 1.55.0+dfsg-1ubuntu3 [102 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/universe libboost-graph-dev ppc64el 1.55.0.1~ubuntu1 [2966 B] Get:29 http://ftpmaster.internal/ubuntu/ vivid/universe libf2c2 ppc64el 20090411-2 [60.9 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/universe libf2c2-dev ppc64el 20090411-2 [185 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.6 MB in 19s (1071 kB/s) Selecting previously unselected package libmagic1:ppc64el. (Reading database ... 11394 files and directories currently installed.) Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1.1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.19-1ubuntu1.1) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.19.2-2ubuntu1_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.19.2-2ubuntu1) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../libglib2.0-0_2.42.0-2_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.42.0-2) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../libpipeline1_1.3.1-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.3.1-1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../libxml2_2.9.1+dfsg1-4ubuntu1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.1+dfsg1-4ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-8_ppc64el.deb ... Unpacking groff-base (1.22.2-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5ubuntu1_ppc64el.deb ... Unpacking bsdmainutils (9.0.5ubuntu1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.0.2-2_ppc64el.deb ... Unpacking man-db (2.7.0.2-2) ... Selecting previously unselected package libicu52:ppc64el. Preparing to unpack .../libicu52_52.1-6_ppc64el.deb ... Unpacking libicu52:ppc64el (52.1-6) ... Selecting previously unselected package libboost-regex1.55.0:ppc64el. Preparing to unpack .../libboost-regex1.55.0_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-regex1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Selecting previously unselected package libboost-graph1.55.0:ppc64el. Preparing to unpack .../libboost-graph1.55.0_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-graph1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... 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Preparing to unpack .../libboost-graph1.55-dev_1.55.0+dfsg-1ubuntu3_ppc64el.deb ... Unpacking libboost-graph1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Selecting previously unselected package libboost-graph-dev:ppc64el. Preparing to unpack .../libboost-graph-dev_1.55.0.1~ubuntu1_ppc64el.deb ... Unpacking libboost-graph-dev:ppc64el (1.55.0.1~ubuntu1) ... Selecting previously unselected package libf2c2. Preparing to unpack .../libf2c2_20090411-2_ppc64el.deb ... Unpacking libf2c2 (20090411-2) ... Selecting previously unselected package libf2c2-dev. Preparing to unpack .../libf2c2-dev_20090411-2_ppc64el.deb ... Unpacking libf2c2-dev (20090411-2) ... Setting up libmagic1:ppc64el (1:5.19-1ubuntu1.1) ... Setting up libasprintf0c2:ppc64el (0.19.2-2ubuntu1) ... Setting up libglib2.0-0:ppc64el (2.42.0-2) ... No schema files found: doing nothing. Setting up libpipeline1:ppc64el (1.3.1-1) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-4ubuntu1) ... Setting up groff-base (1.22.2-8) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.7.0.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libicu52:ppc64el (52.1-6) ... Setting up libboost-regex1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-serialization1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-test1.55.0:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libcroco3:ppc64el (0.6.8-3) ... Setting up libunistring0:ppc64el (0.9.3-5ubuntu3) ... Setting up file (1:5.19-1ubuntu1.1) ... Setting up gettext-base (0.19.2-2ubuntu1) ... Setting up gettext (0.19.2-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.98-0ubuntu2) ... Setting up debhelper (9.20141003ubuntu1) ... Setting up libboost1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-dev:ppc64el (1.55.0.1~ubuntu1) ... Setting up libboost-serialization1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-test1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph1.55-dev:ppc64el (1.55.0+dfsg-1ubuntu3) ... Setting up libboost-graph-dev:ppc64el (1.55.0.1~ubuntu1) ... Setting up libf2c2 (20090411-2) ... Setting up libf2c2-dev (20090411-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-10ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-19ubuntu1 g++-4.9_4.9.1-19ubuntu1 binutils_2.24.90.20141023-1ubuntu1 libstdc++-4.9-dev_4.9.1-19ubuntu1 libstdc++6_4.9.1-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Sun Sep 7 19:49:52 2014 UTC using RSA key ID 9A0C52FA gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./disulfinder_1.2.11-4.dsc dpkg-source: info: extracting disulfinder in disulfinder-1.2.11 dpkg-source: info: unpacking disulfinder_1.2.11.orig.tar.gz dpkg-source: info: unpacking disulfinder_1.2.11-4.debian.tar.xz dpkg-source: info: applying hardening.patch dpkg-source: info: applying variable_length_array dpkg-source: info: applying unknown_escape dpkg-buildpackage: source package disulfinder dpkg-buildpackage: source version 1.2.11-4 dpkg-buildpackage: source distribution unstable dpkg-source --before-build disulfinder-1.2.11 dpkg-buildpackage: host architecture ppc64el /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 distclean make[1]: Entering directory '/build/buildd/disulfinder-1.2.11' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src' make -C NN clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/NN' make -C Common clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Common' make -C eig clean make[4]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[4]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Common' make -C SVM clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/SVM' cd SVM && make clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src' rm -f *.[12345678] *.[12345678].gz #if [ -d "disulfind" ]; then rm -rf disulfind; fi if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi rm -rf patch-stamp \ initial-clean-stamp \ "disulfinder-1.2.11.tar.gz" \ .pc make[1]: Leaving directory '/build/buildd/disulfinder-1.2.11' dh_clean rm -f debian/disulfinder.substvars rm -f debian/disulfinder.*.debhelper rm -rf debian/disulfinder/ rm -f debian/disulfinder-data.substvars rm -f debian/disulfinder-data.*.debhelper rm -rf debian/disulfinder-data/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make -j1 make[1]: Entering directory '/build/buildd/disulfinder-1.2.11' make -C disulfind/src disulfinder make[2]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src' g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/utils.h:2:0, from Input/GlobalDescriptor.cpp:3: Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] static const char *aa_three_codes[23] = { ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/utils.h:2:0, from Input/createBRNNDataset.h:1, from Input/createBRNNDataset.cpp:2: Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] static const char *aa_three_codes[23] = { ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/utils.h:2:0, from Input/createKernelDataset.h:1, from Input/createKernelDataset.cpp:2: Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] static const char *aa_three_codes[23] = { ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o Output/makeHTMLOutput.cpp: In function 'void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)': Output/makeHTMLOutput.cpp:162:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"Second","Third"}; ^ Output/makeHTMLOutput.cpp:162:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o Output/makeASCIIOutput.cpp: In function 'void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)': Output/makeASCIIOutput.cpp:144:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"SECOND","THIRD"}; ^ Output/makeASCIIOutput.cpp:144:40: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o In file included from BRNN/RNNs/DataSet.cpp:1:0: BRNN/RNNs/DataSet.h:37:2: warning: 'typedef' was ignored in this declaration }; ^ In file included from BRNN/RNNs/DataSet.cpp:1:0: BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)': BRNN/RNNs/DataSet.h:86:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ^ BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()': BRNN/RNNs/DataSet.h:116:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ^ BRNN/RNNs/DataSet.h:135:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ^ BRNN/RNNs/DataSet.cpp: In constructor 'DataSet::DataSet(const char*, const char*)': BRNN/RNNs/DataSet.cpp:69:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos == string::npos) ^ BRNN/RNNs/DataSet.cpp: In member function 'bool DataSet::loadInstances(const char*)': BRNN/RNNs/DataSet.cpp:141:7: warning: unused variable 'ng' [-Wunused-variable] int ng = 1; ^ BRNN/RNNs/DataSet.cpp: At global scope: BRNN/RNNs/DataSet.cpp:14:12: warning: 'int one(const dirent*)' defined but not used [-Wunused-function] static int one(const struct dirent* unused) { ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o BRNN/RNNs/DPAG.cpp: In function 'float PRMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:48:7: warning: unused variable 'global_predicted_positives' [-Wunused-variable] int global_predicted_positives = boost::num_edges(g), ^ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable 'global_actual_positives' [-Wunused-variable] global_actual_positives = boost::num_edges(gtarget), ^ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable 'graphNode' [-Wunused-variable] Vertex_d graphNode, targetNode; ^ BRNN/RNNs/DPAG.cpp: In function 'float PrecisionMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:302:12: warning: unused variable 'graphNode' [-Wunused-variable] Vertex_d graphNode, targetNode; ^ BRNN/RNNs/DPAG.cpp: In function 'std::pair globalPRMeasure(const DPAG&, const DPAG&, int&, int&, int&, int&, int&, int&, float&)': BRNN/RNNs/DPAG.cpp:361:12: warning: unused variable 'graphNode' [-Wunused-variable] Vertex_d graphNode, targetNode, targetNode1; ^ BRNN/RNNs/DPAG.cpp: In function 'ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:560:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] false_positives + false_negatives == ^ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable 'weight' [-Wunused-variable] float weight = 1.0 / boost::num_vertices(gpred); ^ BRNN/RNNs/DPAG.cpp: In function 'float RecallMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:573:12: warning: unused variable 'graphNode' [-Wunused-variable] Vertex_d graphNode, targetNode; ^ BRNN/RNNs/DPAG.cpp: In function 'bool equal(const DPAG&, const DPAG&)': BRNN/RNNs/DPAG.cpp:746:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i, boost::property >, boost::adjacency_list, boost::property > > dpag_to_rnndpag(const DPAG&)': BRNN/RNNs/DPAG.cpp:832:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(vertex_id[*v_i] != n_vertices-1) { ^ BRNN/RNNs/DPAG.cpp:839:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(children.front() == vertex_id[*v_i]+1) ^ BRNN/RNNs/DPAG.cpp:844:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i, boost::property >, boost::adjacency_list, boost::property > >&)': BRNN/RNNs/DPAG.cpp:878:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] VertexId vertex_id = boost::get(boost::vertex_index, g);; ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_config(const string&)': BRNN/RNNs/Options.cpp:30:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:36:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:42:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:47:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:61:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:79:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:85:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:90:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:99:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(_input_mask.size() != _input_dimension) ^ BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_args(int, char**)': BRNN/RNNs/Options.cpp:138:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:144:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:150:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:155:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:169:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:187:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:193:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:198:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ^ BRNN/RNNs/Options.cpp:207:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(_input_mask.size() != _input_dimension) ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o In file included from BRNN/protein_util.cpp:1:0: BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] Coordinate3D _coord; // residue representative coordinates ^ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): ^ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): ^ BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] Coordinate3D _coord; // residue representative coordinates ^ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] int _bp1, _bp2; // bridge partners ^ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner ^ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^ BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)': BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder] Coordinate3D _baricentre; // baricentrum of C_alpha atoms set ^ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment ^ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] SSegment(char symbol): ^ In file included from /usr/include/c++/4.9/cassert:43:0, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp: In member function 'void Chain::setSShydrophobicity()': BRNN/protein_util.cpp:365:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assert(resHydrScales.size() == numResidues()); ^ BRNN/protein_util.cpp:380:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; ^ In file included from /usr/include/c++/4.9/cassert:43:0, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp:386:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] assert(hAvg.size() == (*c_it).numResidues()); ^ BRNN/protein_util.cpp:391:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i=0 && i < pssm.size()) ^ BRNN/rnn_util.cpp: In function 'void rnn_predict_disulphides(const string&, const string&, const string&, const string&, const string&, const string&, int)': BRNN/rnn_util.cpp:359:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] require(B == boost::num_edges(candidate) && ^ BRNN/rnn_util.cpp:348:16: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] VertexId vertex_id = boost::get(boost::vertex_index, candidate); ^ BRNN/rnn_util.cpp:405:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j=0; j *nodes = it.currenTONodes(); ^ In file included from BRNN/rnn_util.cpp:5:0: BRNN/RNNs/RecursiveNN.h: In instantiation of 'RecursiveNN::RecursiveNN(const char*) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]': BRNN/rnn_util.cpp:88:73: required from here BRNN/RNNs/RecursiveNN.h:1018:13: warning: unused variable 'trasd' [-Wunused-variable] TrasdType trasd = Options::instance()->getTrasductionType(); ^ In file included from BRNN/rnn_util.cpp:5:0: BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable 'indexes' set but not used [-Wunused-but-set-variable] std::pair indexes = Options::instance()->getLayersIndexes(); ^ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable 'default_precision' [-Wunused-variable] int default_precision = is.precision(); ^ In file included from BRNN/rnn_util.cpp:6:0: BRNN/RNNs/StructureSearch.h: In instantiation of 'std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]': BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:977:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i<_nodesInputs.size(); ++i) ^ BRNN/RNNs/StructureSearch.h:984:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i::fPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/RecursiveNN.h:1356:39: required from 'void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]' BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!"); ^ BRNN/RNNs/RecursiveNN.h:1415:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { ^ BRNN/RNNs/RecursiveNN.h:1418:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { ^ BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] VertexId vertex_id = boost::get(boost::vertex_index, sdag); ^ BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN::bPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/RecursiveNN.h:1359:56: required from 'void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]' BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int t=0; t_encodedInput.size(), "Error!"); ^ BRNN/RNNs/RecursiveNN.h:1492:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { ^ BRNN/RNNs/RecursiveNN.h:1495:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { ^ BRNN/RNNs/RecursiveNN.h:1465:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] VertexId vertex_id = boost::get(boost::vertex_index, sdag); ^ In file included from BRNN/rnn_util.cpp:6:0: BRNN/RNNs/StructureSearch.h: In instantiation of 'float StructureSearch::RNNMeasure(const DPAG&, RNN*, std::vector&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/StructureSearch.h:990:66: required from 'std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]' BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:186:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' [-Wconversion-null] return false; ^ g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c CommonMethods.cpp -o CommonMethods.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c ConfusionMatrix.cpp -o ConfusionMatrix.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Exception.cpp -o Exception.o g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/rg.o eig/rg.c g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o cc -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o eig/d_sign.o eig/d_sign.c ar rvs libCommon.a Vector.o Util.o CommonMethods.o ConfusionMatrix.o Exception.o Statistics.o eig/balanc.o eig/balbak.o eig/cdiv.o eig/elmhes.o eig/eltran.o eig/hqr.o eig/hqr2.o eig/rg.o coords.o eig/d_sign.o ar: creating libCommon.a a - Vector.o a - Util.o a - CommonMethods.o a - ConfusionMatrix.o a - Exception.o a - Statistics.o a - eig/balanc.o a - eig/balbak.o a - eig/cdiv.o a - eig/elmhes.o a - eig/eltran.o a - eig/hqr.o a - eig/hqr2.o a - eig/rg.o a - coords.o a - eig/d_sign.o make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src/Common' g++ -D_FORTIFY_SOURCE=2 -g -O3 -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c disulfinder.cpp -o disulfinder.o In file included from Input/utils.h:2:0, from disulfinder.cpp:8: Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^ Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] static const char *aa_three_codes[23] = { ^ g++ -o disulfinder disulfinder.o Input/GlobalDescriptor.o Input/createBRNNDataset.o Input/createKernelDataset.o Input/makeWindow.o Input/makeSparseVector.o Input/Protein.o Input/buildXfolds.o SVM/SVMClassifier.o Output/makeHTMLOutput.o Output/utils.o Output/makeASCIIOutput.o FSA-Alignment/fsa.o FSA-Alignment/viterbi_aligner.o NN/multi-array.o NN/array.o NN/brnn-model.o NN/brnn-test.o BRNN/RNNs/Node.o BRNN/RNNs/StructureSearch.o BRNN/RNNs/DataSet.o BRNN/RNNs/DPAG.o BRNN/RNNs/Options.o BRNN/protein_util.o BRNN/blast_util.o BRNN/rnn_util.o -Wl,-Bsymbolic-functions -Wl,-z,relro -LCommon/ -lCommon make[2]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src' sed -e 's|__datadir__||g;s|__docdir__|/usr/share/doc/disulfinder|g;s|__pkgdatadir__||g;s|__PREFIX__|/usr|g;s|__sysconfdir__||g;s|__VERSION__|1.2.11|g;' "disulfinder.pod" | \ pod2man -c 'User Commands' -r '1.2.11' -name DISULFINDER > "disulfinder.1" make[1]: Leaving directory '/build/buildd/disulfinder-1.2.11' dh_auto_test -a /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f debian/disulfinder.substvars rm -f debian/disulfinder.*.debhelper rm -rf debian/disulfinder/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/buildd/disulfinder-1.2.11' /usr/bin/make DESTDIR=/build/buildd/disulfinder-1.2.11/debian/disulfinder prefix=/usr install make[2]: Entering directory '/build/buildd/disulfinder-1.2.11' /usr/bin/make -C disulfind/src install make[3]: Entering directory '/build/buildd/disulfinder-1.2.11/disulfind/src' mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/bin cp disulfinder /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/bin/ mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models cp -r ../Models /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ && find /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \; rm -rf /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5 rm -rf /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Predictions rm -rf /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/tmp make[3]: Leaving directory '/build/buildd/disulfinder-1.2.11/disulfind/src' mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1/ mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples/ make[2]: Leaving directory '/build/buildd/disulfinder-1.2.11' make[1]: Leaving directory '/build/buildd/disulfinder-1.2.11' debian/rules override_dh_install make[1]: Entering directory '/build/buildd/disulfinder-1.2.11' dh_install mkdir -p /build/buildd/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder mv /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder /build/buildd/disulfinder-1.2.11/debian/disulfinder-data/usr/share/ make[1]: Leaving directory '/build/buildd/disulfinder-1.2.11' dh_installdocs -a cd 'debian/upstream/..' && find 'upstream' \( -type f -or -type l \) -and ! -empty -print0 | xargs -0 -I {} cp --parents -dp {} /build/buildd/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder chown -R 0:0 debian/disulfinder/usr/share/doc chmod -R go=rX debian/disulfinder/usr/share/doc chmod -R u\+rw debian/disulfinder/usr/share/doc install -g 0 -o 0 -m 644 -p debian/copyright debian/disulfinder/usr/share/doc/disulfinder/copyright dh_installchangelogs -a install -o 0 -g 0 -p -m644 debian/changelog debian/disulfinder/usr/share/doc/disulfinder/changelog.Debian dh_installman -a man --recode UTF-8 ./disulfinder\.1 > disulfinder\.1\.new chmod 644 disulfinder.1.new mv -f disulfinder.1.new disulfinder.1 dh_perl -a dh_link -a dh_compress -a cd debian/disulfinder chmod a-x usr/share/man/man1/disulfinder.1 usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/doc/disulfinder/changelog.Debian gzip -9nf usr/share/man/man1/disulfinder.1 usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/doc/disulfinder/changelog.Debian cd '/build/buildd/disulfinder-1.2.11' dh_fixperms -a find debian/disulfinder -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/disulfinder ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/disulfinder/usr/share/doc -type f ! -regex 'debian/disulfinder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/disulfinder/usr/share/man debian/disulfinder/usr/man/ debian/disulfinder/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/disulfinder/usr/lib/powerpc64le-linux-gnu/perl5/5.20 debian/disulfinder/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/disulfinder/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/disulfinder/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_strip -a dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: disulfinder dh_strip debug symbol extraction: packages to act on: disulfinder dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `disulfinder-dbgsym' in `../disulfinder-dbgsym_1.2.11-4_ppc64el.ddeb'. strip --remove-section=.comment --remove-section=.note debian/disulfinder/usr/bin/disulfinder dh_makeshlibs -a rm -f debian/disulfinder/DEBIAN/shlibs dh_shlibdeps -a install -o 0 -g 0 -d debian/disulfinder/DEBIAN dpkg-shlibdeps -Tdebian/disulfinder.substvars debian/disulfinder/usr/bin/disulfinder dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/disulfinder.substvars dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/disulfinder dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/disulfinder/DEBIAN/control chown 0:0 debian/disulfinder/DEBIAN/control dh_md5sums -a (cd debian/disulfinder >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/disulfinder/DEBIAN/md5sums chown 0:0 debian/disulfinder/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/disulfinder .. INFO: pkgstriptranslations version 121 pkgstriptranslations: processing disulfinder (in debian/disulfinder); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/disulfinder/DEBIAN/control, package disulfinder, directory debian/disulfinder pkgstripfiles: PNG optimization for package disulfinder took 0 s dpkg-deb: warning: 'debian/disulfinder/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `disulfinder' in `../disulfinder_1.2.11-4_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../disulfinder_1.2.11-4_ppc64el.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build disulfinder-1.2.11 dpkg-buildpackage: binary-only upload (no source included) ****************************************************************************** Build finished at 20141024-0912 Publishing debug debs. chroot-autobuild/build/buildd/disulfinder_1.2.11-4_ppc64el.deb: new debian package, version 2.0. size 240334 bytes: control archive=1229 bytes. 1378 bytes, 25 lines control 550 bytes, 7 lines md5sums Package: disulfinder Version: 1.2.11-4 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 814 Depends: libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.9), disulfinder-data Section: science Priority: optional Homepage: http://disulfind.dsi.unifi.it/ Description: cysteines disulfide bonding state and connectivity predictor 'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. . 'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern. chroot-autobuild/build/buildd/disulfinder_1.2.11-4_ppc64el.deb: drwxr-xr-x root/root 0 2014-10-24 09:12 ./ drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/ drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/bin/ -rwxr-xr-x root/root 770568 2014-10-24 09:12 ./usr/bin/disulfinder drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/ drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/man/man1/ -rw-r--r-- root/root 3634 2014-10-24 09:12 ./usr/share/man/man1/disulfinder.1.gz drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/doc/disulfinder/ drwxr-xr-x root/root 0 2014-09-07 15:46 ./usr/share/doc/disulfinder/upstream/ -rw-r--r-- root/root 1302 2014-09-07 03:56 ./usr/share/doc/disulfinder/upstream/metadata -rw-r--r-- root/root 2159 2014-09-07 15:42 ./usr/share/doc/disulfinder/copyright drwxr-xr-x root/root 0 2014-10-24 09:12 ./usr/share/doc/disulfinder/examples/ -rw-r--r-- root/root 5977 2014-10-24 09:12 ./usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb.gz -rw-r--r-- root/root 3609 2014-10-24 09:12 ./usr/share/doc/disulfinder/examples/res_id_41483.expected_result -rw-r--r-- root/root 888 2014-09-07 15:43 ./usr/share/doc/disulfinder/changelog.Debian.gz disulfinder_1.2.11-4_ppc64el.changes: Format: 1.8 Date: Sun, 07 Sep 2014 09:56:52 +0200 Source: disulfinder Binary: disulfinder disulfinder-data Architecture: ppc64el Version: 1.2.11-4 Distribution: vivid-proposed Urgency: medium Maintainer: Ubuntu Build Daemon Changed-By: Laszlo Kajan Description: disulfinder - cysteines disulfide bonding state and connectivity predictor disulfinder-data - data files for predictor of disulfide bonds in proteins Closes: 741559 Changes: disulfinder (1.2.11-4) unstable; urgency=medium . * Included patch to solve 'FTBFS with clang' (Closes: #741559) * Patched out 'unrecognized escape sequences' Checksums-Sha1: 671cacf2da45a8c484c15cfcb9cc89dbb4a31775 240334 disulfinder_1.2.11-4_ppc64el.deb Checksums-Sha256: 2100103231f0316be7ba13d2214bd29e0ca675ed5b1d9a23a88a99bd4d238fdb 240334 disulfinder_1.2.11-4_ppc64el.deb Files: ad95fe99aaa8d72643a6ee89d3b3d719 240334 science optional disulfinder_1.2.11-4_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20141024-0912 Build needed 00:01:22, 70852k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6487754'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6487754/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6487754'] Unmounting chroot for build PACKAGEBUILD-6487754... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6487754'] Removing build PACKAGEBUILD-6487754