RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux toyol 3.2.0-54-generic #82-Ubuntu SMP Tue Sep 10 20:08:42 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.2. Syncing the system clock with the buildd NTP service... 6 Feb 01:20:20 ntpdate[30641]: adjust time server 10.211.37.1 offset -0.000071 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5559323', '/home/buildd/filecache-default/85437d411726979c3d865ddb70b8896a411f3906'] Unpacking chroot for build PACKAGEBUILD-5559323 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5559323'] Mounting chroot for build PACKAGEBUILD-5559323 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5559323', 'deb http://ftpmaster.internal/ubuntu trusty main universe', 'deb http://ftpmaster.internal/ubuntu trusty-security main universe', 'deb http://ftpmaster.internal/ubuntu trusty-updates main universe', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-5559323 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5559323', 'i386'] Updating debian chroot for build PACKAGEBUILD-5559323 Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty-updates InRelease Get:1 http://archive-team.internal trusty Release [723 B] Ign http://ftpmaster.internal trusty-proposed InRelease Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:4 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:6 http://archive-team.internal trusty/main i386 Packages Get:7 http://ftpmaster.internal trusty Release [58.5 kB] Ign http://archive-team.internal trusty/main Translation-en Get:8 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:9 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:10 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:11 http://ftpmaster.internal trusty/main i386 Packages [1309 kB] Get:12 http://ftpmaster.internal trusty/universe i386 Packages [5882 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [752 kB] Get:14 http://ftpmaster.internal trusty/universe Translation-en [4052 kB] Get:15 http://ftpmaster.internal trusty-security/main i386 Packages [14 B] Get:16 http://ftpmaster.internal trusty-security/universe i386 Packages [14 B] Get:17 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal trusty-updates/main i386 Packages [14 B] Get:20 http://ftpmaster.internal trusty-updates/universe i386 Packages [14 B] Get:21 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal trusty-proposed/main i386 Packages [38.6 kB] Get:24 http://ftpmaster.internal trusty-proposed/universe i386 Packages [141 kB] Get:25 http://ftpmaster.internal trusty-proposed/main Translation-en [19.9 kB] Get:26 http://ftpmaster.internal trusty-proposed/universe Translation-en [96.8 kB] Fetched 12.5 MB in 6s (1861 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libprocps1 Use 'apt-get autoremove' to remove it. The following NEW packages will be installed: libdebconfclient0 libprocps3 The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils bsdutils cpp cpp-4.8 dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-4.8 gcc gcc-4.8 gcc-4.8-base gnupg gpgv grep gzip ifupdown libapt-pkg4.12 libasan0 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm2 libffi6 libgcc-4.8-dev libgcc1 libgmp10 libgomp1 libgssapi-krb5-2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libmount1 libncurses5 libncursesw5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libplymouth2 libpng12-0 libquadmath0 libselinux1 libsqlite3-0 libss2 libstdc++-4.8-dev libstdc++6 libtinfo5 libudev1 libuuid1 linux-libc-dev login mount multiarch-support ncurses-base ncurses-bin passwd perl perl-base perl-modules pkgbinarymangler plymouth procps tar udev upstart util-linux 81 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 46.9 MB of archives. After this operation, 2297 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main base-files i386 7.2ubuntu1 [45.1 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main dpkg i386 1.17.5ubuntu3 [1945 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main libc-bin i386 2.18-0ubuntu6 [1100 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libdbus-1-3 i386 1.6.18-0ubuntu3 [131 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main libselinux1 i386 2.2.2-1 [56.6 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main libpam0g i386 1.1.8-1ubuntu2 [55.1 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules-bin i386 1.1.8-1ubuntu2 [30.8 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules i386 1.1.8-1ubuntu2 [232 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main passwd i386 1:4.1.5.1-1ubuntu8 [746 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main libuuid1 i386 2.20.1-5.1ubuntu14 [11.5 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main libblkid1 i386 2.20.1-5.1ubuntu14 [67.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main util-linux i386 2.20.1-5.1ubuntu14 [450 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main libprocps3 i386 1:3.3.9-1ubuntu2 [30.0 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main libncursesw5 i386 5.9+20131221-1ubuntu1 [122 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty/main libtinfo5 i386 5.9+20131221-1ubuntu1 [70.9 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty/main libncurses5 i386 5.9+20131221-1ubuntu1 [93.7 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty/main procps i386 1:3.3.9-1ubuntu2 [203 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main udev i386 204-5ubuntu10 [736 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty/main libudev1 i386 204-5ubuntu10 [36.2 kB] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main ifupdown i386 0.7.47.2ubuntu1 [51.3 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty/main upstart i386 1.11-0ubuntu3 [364 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main libc6-dev i386 2.18-0ubuntu6 [2552 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty/main libc-dev-bin i386 2.18-0ubuntu6 [63.4 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-proposed/main linux-libc-dev i386 3.13.0-7.26 [761 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main libitm1 i386 4.8.2-14ubuntu4 [28.4 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty/main libgomp1 i386 4.8.2-14ubuntu4 [25.0 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main libasan0 i386 4.8.2-14ubuntu4 [64.0 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8-base i386 4.8.2-14ubuntu4 [15.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main libgcc1 i386 1:4.8.2-14ubuntu4 [46.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main libatomic1 i386 4.8.2-14ubuntu4 [8228 B] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main libquadmath0 i386 4.8.2-14ubuntu4 [187 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main cpp-4.8 i386 4.8.2-14ubuntu4 [4448 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++-4.8-dev i386 4.8.2-14ubuntu4 [1043 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main g++-4.8 i386 4.8.2-14ubuntu4 [4811 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main gcc-4.8 i386 4.8.2-14ubuntu4 [4867 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main libgcc-4.8-dev i386 4.8.2-14ubuntu4 [1735 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main libstdc++6 i386 4.8.2-14ubuntu4 [261 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main libgmp10 i386 2:5.1.3+dfsg-1ubuntu1 [230 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main binutils i386 2.24-2ubuntu3 [2109 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libc6 i386 2.18-0ubuntu6 [4017 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main e2fslibs i386 1.42.9-2ubuntu1 [192 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main e2fsprogs i386 1.42.9-2ubuntu1 [665 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main findutils i386 4.4.2-7 [237 kB] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main grep i386 2.16-1 [157 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main gzip i386 1.6-3ubuntu1 [83.8 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty/main login i386 1:4.1.5.1-1ubuntu8 [302 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main mount i386 2.20.1-5.1ubuntu14 [113 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main ncurses-bin i386 5.9+20131221-1ubuntu1 [135 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main perl i386 5.18.2-2 [2159 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main perl-base i386 5.18.2-2 [1133 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main perl-modules all 5.18.2-2 [2696 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main tar i386 1.27.1-1 [194 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libapt-pkg4.12 i386 0.9.14.1ubuntu2 [623 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main gpgv i386 1.4.16-1ubuntu1 [152 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main gnupg i386 1.4.16-1ubuntu1 [593 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main apt i386 0.9.14.1ubuntu2 [954 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main libdebconfclient0 i386 0.187ubuntu1 [6594 B] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main base-passwd i386 3.5.32 [45.6 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main bsdutils i386 1:2.20.1-5.1ubuntu14 [34.1 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main ncurses-base all 5.9+20131221-1ubuntu1 [16.5 kB] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main libcomerr2 i386 1.42.9-2ubuntu1 [62.4 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main libmount1 i386 2.20.1-5.1ubuntu14 [59.7 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main libss2 i386 1.42.9-2ubuntu1 [66.5 kB] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main libffi6 i386 3.0.13-12 [14.3 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/main libsqlite3-0 i386 3.8.2-1ubuntu2 [344 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libdrm2 i386 2.4.52-1 [23.2 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main plymouth i386 0.8.8-0ubuntu14 [98.8 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main libpng12-0 i386 1.2.50-1ubuntu1 [118 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty/main libplymouth2 i386 0.8.8-0ubuntu14 [76.3 kB] Get:70 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libk5crypto3 i386 1.12+dfsg-2ubuntu1 [77.6 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgssapi-krb5-2 i386 1.12+dfsg-2ubuntu1 [111 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libkrb5-3 i386 1.12+dfsg-2ubuntu1 [260 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libkrb5support0 i386 1.12+dfsg-2ubuntu1 [30.1 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main libcurl3-gnutls i386 7.35.0-1ubuntu1 [166 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty/main libpam-runtime all 1.1.8-1ubuntu2 [37.7 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty/main multiarch-support i386 2.18-0ubuntu6 [4486 B] Get:77 http://ftpmaster.internal/ubuntu/ trusty/main apt-transport-https i386 0.9.14.1ubuntu2 [24.9 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty/main cpp i386 4:4.8.2-1ubuntu3 [27.7 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty/main dpkg-dev all 1.17.5ubuntu3 [726 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty/main libdpkg-perl all 1.17.5ubuntu3 [179 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty/main gcc i386 4:4.8.2-1ubuntu3 [4990 B] Get:82 http://ftpmaster.internal/ubuntu/ trusty/main g++ i386 4:4.8.2-1ubuntu3 [1492 B] Get:83 http://ftpmaster.internal/ubuntu/ trusty/main pkgbinarymangler all 119 [28.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.9 MB in 4s (11.6 MB/s) (Reading database ... 11989 files and directories currently installed.) Preparing to replace base-files 6.12ubuntu5 (using .../base-files_7.2ubuntu1_i386.deb) ... Unpacking replacement base-files ... Setting up base-files (7.2ubuntu1) ... Installing new version of config file /etc/debian_version ... (Reading database ... 11989 files and directories currently installed.) Preparing to replace dpkg 1.17.1ubuntu1 (using .../dpkg_1.17.5ubuntu3_i386.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.17.5ubuntu3) ... (Reading database ... 11991 files and directories currently installed.) Preparing to unpack .../libc-bin_2.18-0ubuntu6_i386.deb ... Unpacking libc-bin (2.18-0ubuntu6) over (2.18-0ubuntu2) ... Preparing to unpack .../libc6_2.18-0ubuntu6_i386.deb ... Unpacking libc6:i386 (2.18-0ubuntu6) over (2.18-0ubuntu2) ... Preparing to unpack .../libgcc1_1%3a4.8.2-14ubuntu4_i386.deb ... Unpacking libgcc1:i386 (1:4.8.2-14ubuntu4) over (1:4.8.2-10ubuntu2) ... Preparing to unpack .../gcc-4.8-base_4.8.2-14ubuntu4_i386.deb ... 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Preparing to unpack .../passwd_1%3a4.1.5.1-1ubuntu8_i386.deb ... Unpacking passwd (1:4.1.5.1-1ubuntu8) over (1:4.1.5.1-1ubuntu6) ... Setting up passwd (1:4.1.5.1-1ubuntu8) ... (Reading database ... 11992 files and directories currently installed.) Preparing to unpack .../libuuid1_2.20.1-5.1ubuntu14_i386.deb ... Unpacking libuuid1:i386 (2.20.1-5.1ubuntu14) over (2.20.1-5.1ubuntu11) ... Setting up libuuid1:i386 (2.20.1-5.1ubuntu14) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11992 files and directories currently installed.) Preparing to unpack .../libblkid1_2.20.1-5.1ubuntu14_i386.deb ... Unpacking libblkid1:i386 (2.20.1-5.1ubuntu14) over (2.20.1-5.1ubuntu11) ... Setting up libblkid1:i386 (2.20.1-5.1ubuntu14) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11992 files and directories currently installed.) Preparing to unpack .../util-linux_2.20.1-5.1ubuntu14_i386.deb ... Unpacking util-linux (2.20.1-5.1ubuntu14) over (2.20.1-5.1ubuntu11) ... Setting up util-linux (2.20.1-5.1ubuntu14) ... Installing new version of config file /etc/cron.weekly/fstrim ... Selecting previously unselected package libprocps3:i386. (Reading database ... 11992 files and directories currently installed.) Preparing to unpack .../libprocps3_1%3a3.3.9-1ubuntu2_i386.deb ... Unpacking libprocps3:i386 (1:3.3.9-1ubuntu2) ... Preparing to unpack .../libncursesw5_5.9+20131221-1ubuntu1_i386.deb ... Unpacking libncursesw5:i386 (5.9+20131221-1ubuntu1) over (5.9+20130608-1ubuntu1) ... Preparing to unpack .../libtinfo5_5.9+20131221-1ubuntu1_i386.deb ... Unpacking libtinfo5:i386 (5.9+20131221-1ubuntu1) over (5.9+20130608-1ubuntu1) ... Setting up libtinfo5:i386 (5.9+20131221-1ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11998 files and directories currently installed.) Preparing to unpack .../libncurses5_5.9+20131221-1ubuntu1_i386.deb ... Unpacking libncurses5:i386 (5.9+20131221-1ubuntu1) over (5.9+20130608-1ubuntu1) ... Setting up libncurses5:i386 (5.9+20131221-1ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... (Reading database ... 11998 files and directories currently installed.) Preparing to unpack .../procps_1%3a3.3.9-1ubuntu2_i386.deb ... invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (1:3.3.9-1ubuntu2) over (1:3.3.8-2ubuntu3) ... Preparing to unpack .../udev_204-5ubuntu10_i386.deb ... Adding 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' Unpacking udev (204-5ubuntu10) over (204-5ubuntu6) ... Preparing to unpack .../libudev1_204-5ubuntu10_i386.deb ... Unpacking libudev1:i386 (204-5ubuntu10) over (204-5ubuntu6) ... Preparing to unpack .../ifupdown_0.7.47.2ubuntu1_i386.deb ... Unpacking ifupdown (0.7.47.2ubuntu1) over (0.7.47.1ubuntu1) ... Preparing to unpack .../upstart_1.11-0ubuntu3_i386.deb ... Unpacking upstart (1.11-0ubuntu3) over (1.11-0ubuntu1) ... 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Setting up dpkg-dev (1.17.5ubuntu3) ... Processing triggers for libc-bin (2.18-0ubuntu6) ... Processing triggers for initramfs-tools (0.103ubuntu3) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5559323', 'i386', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=universe', 'discosnp_1.0.1-1.dsc'] Initiating build PACKAGEBUILD-5559323 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-54-generic #82-Ubuntu SMP Tue Sep 10 20:08:42 UTC 2013 i686 Automatic build of discosnp_1.0.1-1 on toyol by sbuild/i386 1.170.5 Build started at 20140206-0120 ****************************************************************************** discosnp_1.0.1-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), bc, zlib1g-dev Checking for already installed source dependencies... debhelper: missing bc: missing zlib1g-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper bc zlib1g-dev Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libprocps1 Use 'apt-get autoremove' to remove it. The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base install-info intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof bc bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base install-info intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal zlib1g-dev 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 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Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libmpdec2:i386 (2.4.0-6) ... Setting up libpython3.3-stdlib:i386 (3.3.4~rc1-1ubuntu1) ... Setting up python3.3-minimal (3.3.4~rc1-1ubuntu1) ... Setting up libasprintf0c2:i386 (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:i386 (2.39.4-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:i386 (1.2.6-1) ... Setting up libxml2:i386 (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-5) ... 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 (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:i386 (0.6.8-2ubuntu1) ... Setting up libunistring0:i386 (0.9.3-5ubuntu3) ... 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Toolchain package versions: libc6-dev_2.18-0ubuntu6 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu3 gcc-4.8_4.8.2-14ubuntu4 g++-4.8_4.8.2-14ubuntu4 binutils_2.24-2ubuntu3 libstdc++-4.8-dev_4.8.2-14ubuntu4 libstdc++6_4.8.2-14ubuntu4 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Wed Feb 5 07:31:39 2014 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./discosnp_1.0.1-1.dsc dpkg-source: info: extracting discosnp in discosnp-1.0.1 dpkg-source: info: unpacking discosnp_1.0.1.orig.tar.xz dpkg-source: info: unpacking discosnp_1.0.1-1.debian.tar.xz dpkg-source: info: applying fix_build dpkg-buildpackage: source package discosnp dpkg-buildpackage: source version 1.0.1-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build discosnp-1.0.1 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/discosnp-1.0.1' debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' cd minia && make clean make[2]: Entering directory `/build/buildd/discosnp-1.0.1/minia' rm -rf *.o make[2]: Leaving directory `/build/buildd/discosnp-1.0.1/minia' cd kissnp2 && make clean make[2]: Entering directory `/build/buildd/discosnp-1.0.1/kissnp2' rm -rf *.o ../minia/*.o make[2]: Leaving directory `/build/buildd/discosnp-1.0.1/kissnp2' cd kissreads && make clean make[2]: Entering directory `/build/buildd/discosnp-1.0.1/kissreads' rm -rf ./src/*.o kissreads make[2]: Leaving directory `/build/buildd/discosnp-1.0.1/kissreads' rm -f output_analyses/discoSnp_to_genotypes rm -f output_analyses/discoSnp_to_csv rm -f kissnp2/kissnp2 rm -f kissreads/kissreads rm -f kissreads/kissreads.1 rm -f kissnp2/kissnp2.1 dh_clean make[1]: Leaving directory `/build/buildd/discosnp-1.0.1' debian/rules build debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/discosnp-1.0.1' debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' dh_auto_build cd kissnp2 && make k=29 make[2]: Entering directory `/build/buildd/discosnp-1.0.1/kissnp2' g++ -o ../minia/Pool.o -c ../minia/Pool.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Bank.o -c ../minia/Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Bank.cpp: In member function 'int KmersBuffer::readkmers()': ../minia/Bank.cpp:922:65: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof( char),block_size, binary_read_file); // read a block of sequences into the buffer ^ g++ -o ../minia/Bloom.o -c ../minia/Bloom.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Bloom.cpp: In member function 'void Bloom::load(char*)': ../minia/Bloom.cpp:257:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(blooma, sizeof(unsigned char), nchar, file_data); ^ g++ -o ../minia/Hash16.o -c ../minia/Hash16.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Terminator.o -c ../minia/Terminator.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Kmer.o -c ../minia/Kmer.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Traversal.o -c ../minia/Traversal.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Traversal.cpp: In member function 'bool MonumentTraversal::find_starting_kmer(kmer_type, kmer_type&)': ../minia/Traversal.cpp:343:66: warning: format '%d' expects a matching 'int' argument [-Wformat=] if (debug) printf("strand %d shouldnt continue\n"); ^ ../minia/Traversal.cpp:357:72: warning: format '%d' expects a matching 'int' argument [-Wformat=] if (debug) printf("strand %d nothing more to explore\n"); ^ g++ -o ../minia/LinearCounter.o -c ../minia/LinearCounter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Set.o -c ../minia/Set.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Set.cpp: In member function 'void AssocSet::print_total_size()': ../minia/Set.cpp:132:48: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] printf("Assoc set size: %li\n",liste.size()); ^ ../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] printf("Assoc set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity()); ^ ../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ); ^ ../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] ../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] ../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp: In member function 'void AssocPairedSet::print_total_size()': ../minia/Set.cpp:296:55: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] printf("Assoc paired set size: %li\n",liste.size()); ^ ../minia/Set.cpp:297:110: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] printf("Assoc paired set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity()); ^ ../minia/Set.cpp:297:110: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ); ^ ../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] ../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=] ../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=] ../minia/Set.cpp: In member function 'void AssocPairedSet::load(char*)': ../minia/Set.cpp:288:82: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data); ^ g++ -o ../minia/Utils.o -c ../minia/Utils.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)': ../minia/Utils.cpp:434:96: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] printf("Inaccurate estimation, restarting with %d MB RAM\n",(2*nbytes_memory)/1024/1024); ^ ../minia/Utils.cpp: In instantiation of 'Bloom* bloom_create_bloo1(T*, bool) [with T = BloomCpt]': ../minia/Utils.cpp:162:85: required from here ../minia/Utils.cpp:125:81: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'off_t {aka long int}' [-Wformat=] printf("nelem %lli nbits %g \n",SolidKmers->nb_elements(),NBITS_PER_KMER); ^ ../minia/Utils.cpp: In function 'void end_kmer_count_partition(bool, Hash16*)': ../minia/Utils.cpp:182:42: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_write), 0); //erase previous file ^ ../minia/Utils.cpp:194:54: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&cptk, sizeof(cptk), 1, F_kmercpt_read); ^ ../minia/Utils.cpp:220:45: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_read), 0); //erase previous file ^ g++ -o ../minia/SortingCount.o -c ../minia/SortingCount.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)': ../minia/SortingCount.cpp:52:50: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] getcwd(current_path,sizeof(current_path)); ^ ../minia/SortingCount.cpp:248:52: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system("echo 3 > /proc/sys/vm/drop_caches"); ^ ../minia/SortingCount.cpp:469:56: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system("echo 3 > /proc/sys/vm/drop_caches"); ^ g++ -o ../minia/Debloom.o -c ../minia/Debloom.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Debloom.cpp: In function 'Set* load_false_positives_cascading4()': ../minia/Debloom.cpp:369:89: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=] printf("\nInserted %lld (estimated, %llu) kmers in B3.\n", addKmers, estimated_T2_size); ^ ../minia/Debloom.cpp:393:89: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=] printf("\nInserted %lld (estimated, %lld) kmers in B4.\n", addKmers, estimated_T3_size); ^ ../minia/Debloom.cpp:423:115: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=] printf("\nInserted %lld (estimated, %lld) kmers in T4.\n\n", addKmers, (uint64_t)fp->false_positives->capacity()); ^ ../minia/Debloom.cpp: In function 'void end_debloom_partition(bool)': ../minia/Debloom.cpp:30:39: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_debloom_write), 0); //erase previous file ^ g++ -o ../minia/OAHash.o -c ../minia/OAHash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o Kmer_for_kissnp2.o -c Kmer_for_kissnp2.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o SNP.o -c SNP.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER SNP.cpp: In member function 'void Bubble::find_bubbles(const char*, int, int)': SNP.cpp:846:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] {printf("%c \t %llu %%",13,(nb*100)/nbel); ^ g++ -o filter.o -c filter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o commons.o -c commons.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o kissnp2 ../minia/Pool.o ../minia/Bank.o ../minia/Bloom.o ../minia/Hash16.o ../minia/Terminator.o ../minia/Kmer.o ../minia/Traversal.o ../minia/LinearCounter.o ../minia/Set.o ../minia/Utils.o ../minia/SortingCount.o ../minia/Debloom.o ../minia/OAHash.o Kmer_for_kissnp2.o SNP.o filter.o IterativeExtensions.o commons.o kissnp2.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-Bsymbolic-functions -Wl,-z,relro kissnp2.cpp:70:1: warning: this decimal constant is unsigned only in ISO C90 [enabled by default] int64_t genome_size = 3000000000; ^ kissnp2.cpp: In function 'int main(int, char**)': kissnp2.cpp:114:62: warning: too many arguments for format [-Wformat-extra-args] printf("This is kissnp2, version 2.1.1.5\n", getVersion()); ^ kissnp2.cpp:245:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'unsigned int' [-Wformat=] printf("Max kmer size on this compiled version is %lu\n",sizeof(kmer_type)*2); ^ make[2]: Leaving directory `/build/buildd/discosnp-1.0.1/kissnp2' cd kissreads && make k=29 make[2]: Entering directory `/build/buildd/discosnp-1.0.1/kissreads' gcc -o src/coherent_algorithm.o -c src/coherent_algorithm.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/commons.o -c src/commons.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/commons.c: In function 'print_rev_comp': src/commons.c:119:2: warning: passing argument 1 of 'fprintf' from incompatible pointer type [enabled by default] for(i=len-1;i>-1;i--)fprintf(out, "%c",comp[(int)s[i]]); ^ In file included from /usr/include/stdio.h:937:0, from ./include/commons.h:47, from src/commons.c:43: /usr/include/i386-linux-gnu/bits/stdio2.h:95:1: note: expected 'struct FILE * __restrict__' but argument is of type 'gzFile' fprintf (FILE *__restrict __stream, const char *__restrict __fmt, ...) ^ gcc -o src/couple.o -c src/couple.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/extension_algorithm.o -c src/extension_algorithm.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/extension_algorithm.c: In function 'read_coherence': src/extension_algorithm.c:346:4: warning: passing argument 1 of 'get_next_sequence_for_fastq' from incompatible pointer type [enabled by default] read_len = get_next_sequence_for_fastq(reads_file, read, quality,line); ^ In file included from src/extension_algorithm.c:47:0: ./include/commons.h:85:5: note: expected 'gzFile' but argument is of type 'struct FILE *' int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * line); ^ src/extension_algorithm.c:348:4: warning: passing argument 1 of 'get_next_fasta_sequence' from incompatible pointer type [enabled by default] read_len = get_next_fasta_sequence(reads_file, read,line); ^ In file included from src/extension_algorithm.c:47:0: ./include/commons.h:83:5: note: expected 'gzFile' but argument is of type 'struct FILE *' int get_next_fasta_sequence (gzFile file, char * read, char * line); ^ gcc -o src/fragment_index.o -c src/fragment_index.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/kissReads.o -c src/kissReads.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/kissReads.c: In function 'main': src/kissReads.c:359:19: warning: assignment makes pointer from integer without a cast [enabled by default] found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt"); ^ src/kissReads.c:364:19: warning: assignment makes pointer from integer without a cast [enabled by default] found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt") || strstr(reads_file_names[i],"fa") || strstr(reads_file_names[i],"fasta") || strstr(reads_file_names[i],"fna"); ^ src/kissReads.c:428:9: warning: passing argument 1 of 'read_coherence' from incompatible pointer type [enabled by default] read_coherence(reads_files[i], reads_file_names[i], size_seeds, min_coverage, results_against_set, number_of_starters, i, quality, nb_events_per_set, number_paths_per_event, sam_out, max_substitutions, no_subsutitution_on_central_position); ^ In file included from src/kissReads.c:46:0: ./include/extension_algorithm.h:52:7: note: expected 'struct FILE *' but argument is of type 'gzFile' float read_coherence (FILE * reads_file, ^ gcc -o src/list.o -c src/list.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/outputs.o -c src/outputs.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/interface_libchash.o -c src/interface_libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/interface_libchash.c: In function 'hash_clear': src/interface_libchash.c:136:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized] specific_free(data); ^ src/interface_libchash.c: In function 'hash_delete': src/interface_libchash.c:170:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized] specific_free(data); ^ gcc -o src/libchash.o -c src/libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ In file included from src/libchash.c:126:0: src/libchash.c: In function 'EntriesUpto': src/libchash.c:468:14: warning: comparison with string literal results in unspecified behavior [-Waddress] assert("" == "word size is too big in EntriesUpto()"); ^ src/libchash.c: In function 'Delete': src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \ ^ ./include/libchash.h:165:40: note: in expansion of macro 'FREE_KEY' FREE_KEY(ht, (bck)->key); } while ( 0 ) ^ src/libchash.c:1119:4: note: in expansion of macro 'SET_BCK_DELETED' SET_BCK_DELETED(ht, ht->posLastFind); /* find set this, how nice */ ^ src/libchash.c: In function 'ClearHashTable': src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \ ^ src/libchash.c:1183:3: note: in expansion of macro 'FREE_KEY' FREE_KEY(ht, bck->key); ^ src/libchash.c: In function 'HashFind': src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); ^ src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] src/libchash.c: In function 'HashFindOrInsert': src/libchash.c:1244:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return Insert(ht, KEY_TRUNC(ht, key), dataInsert, 0); ^ src/libchash.c: In function 'HashInsert': src/libchash.c:1254:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return Insert(ht, KEY_TRUNC(ht, key), data, SAMEKEY_OVERWRITE); ^ src/libchash.c: In function 'HashDelete': src/libchash.c:1264:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return Delete(ht, KEY_TRUNC(ht, key), !FAST_DELETE, 0); ^ src/libchash.c: In function 'HashFirstBucket': src/libchash.c:1289:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if ( !IS_BCK_DELETED(retval) ) ^ src/libchash.c: In function 'HashNextBucket': src/libchash.c:1299:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if ( !IS_BCK_DELETED(retval) ) ^ src/libchash.c: In function 'HashDoLoad': src/libchash.c:1431:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if ( dataRead != NULL ) /* if it's null, we're done */ ^ src/libchash.c: At top level: src/libchash.c:691:18: warning: 'DenseFree' defined but not used [-Wunused-function] static DenseBin *DenseFree(DenseBin *bin, ulong cBuckets) ^ src/libchash.c:710:21: warning: 'DenseInsert' defined but not used [-Wunused-function] static DenseBucket *DenseInsert(DenseBin *bin, DenseBucket *bckInsert, ^ src/libchash.c:739:21: warning: 'DenseFirstBucket' defined but not used [-Wunused-function] static DenseBucket *DenseFirstBucket(DenseIterator *iter, ^ src/libchash.c:748:13: warning: 'DenseWrite' defined but not used [-Wunused-function] static void DenseWrite(FILE *fp, DenseBin *bin, ulong cBuckets) ^ src/libchash.c:767:14: warning: 'DenseRead' defined but not used [-Wunused-function] static ulong DenseRead(FILE *fp, DenseBin **pbin) ^ src/libchash.c:789:14: warning: 'DenseMemory' defined but not used [-Wunused-function] static ulong DenseMemory(ulong cBuckets, ulong cOccupied) ^ src/libchash.c: In function 'HashFind': src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:220:7: note: in expansion of macro 'READ_UL' READ_UL((ht)->fpData, cchData); \ ^ src/libchash.c:1221:4: note: in expansion of macro 'LOAD_AND_RETURN' LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); ^ src/libchash.c: In function 'HashFindLast': src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:220:7: note: in expansion of macro 'READ_UL' READ_UL((ht)->fpData, cchData); \ ^ src/libchash.c:1226:4: note: in expansion of macro 'LOAD_AND_RETURN' LOAD_AND_RETURN(ht, ht->posLastFind); ^ src/libchash.c: In function 'HashFirstBucket': src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:220:7: note: in expansion of macro 'READ_UL' READ_UL((ht)->fpData, cchData); \ ^ src/libchash.c:1290:3: note: in expansion of macro 'LOAD_AND_RETURN' LOAD_AND_RETURN(ht, retval); ^ src/libchash.c: In function 'HashNextBucket': src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:220:7: note: in expansion of macro 'READ_UL' READ_UL((ht)->fpData, cchData); \ ^ src/libchash.c:1300:3: note: in expansion of macro 'LOAD_AND_RETURN' LOAD_AND_RETURN(ht, retval); ^ src/libchash.c: In function 'HashDoLoad': src/libchash.c:1407:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(szMagicKey, 1, 4, fp); ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:1416:4: note: in expansion of macro 'READ_UL' READ_UL(fp, ht->cchKey); ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:1417:4: note: in expansion of macro 'READ_UL' READ_UL(fp, ht->cItems); ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:1418:4: note: in expansion of macro 'READ_UL' READ_UL(fp, ht->cDeletedItems); ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:1421:4: note: in expansion of macro 'READ_UL' READ_UL(fp, cchKey); ^ src/libchash.c:1423:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(rgchKeys, 1, cchKey, fp); ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:1428:7: note: in expansion of macro 'READ_UL' READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ ^ src/libchash.c: In function 'SparseRead': src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:622:4: note: in expansion of macro 'READ_UL' READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ ^ src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^ src/libchash.c:627:3: note: in expansion of macro 'READ_UL' READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); ^ gcc -o src/tree.o -c src/tree.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o kissreads src/coherent_algorithm.o src/commons.o src/couple.o src/extension_algorithm.o src/fragment_index.o src/kissReads.o src/list.o src/outputs.o src/interface_libchash.o src/libchash.o src/tree.o -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wall -lm -O3 -lz ################# # Compilation OK# ################# make[2]: Leaving directory `/build/buildd/discosnp-1.0.1/kissreads' make[1]: Leaving directory `/build/buildd/discosnp-1.0.1' dh_auto_test /usr/bin/fakeroot debian/rules binary debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory `/build/buildd/discosnp-1.0.1' debian/rules:39: warning: overriding commands for target `get-orig-source' debian/rules:12: warning: ignoring old commands for target `get-orig-source' cp output_analyses/discoSnp_to_genotypes.py output_analyses/discoSnp_to_genotypes cp output_analyses/discoSnp_to_csv.py output_analyses/discoSnp_to_csv cd kissnp2 && help2man --help-option=-h --version-string=1.0.1 kissnp2 > kissnp2.1 /bin/sh: 1: help2man: not found make[1]: *** [override_dh_install] Error 127 make[1]: Leaving directory `/build/buildd/discosnp-1.0.1' make: *** [binary] Error 2 dpkg-buildpackage: error: /usr/bin/fakeroot debian/rules binary gave error exit status 2 ****************************************************************************** Build finished at 20140206-0121 FAILED [dpkg-buildpackage died] ****************************************************************************** Finished at 20140206-0121 Build needed 00:00:21, 5564k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5559323'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5559323/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5559323'] Unmounting chroot for build PACKAGEBUILD-5559323... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5559323'] Removing build PACKAGEBUILD-5559323