RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kishi10 3.2.0-95-highbank #135-Ubuntu SMP PREEMPT Tue Nov 10 14:26:08 UTC 2015 armv7l Buildd toolchain package versions: launchpad-buildd_134 python-lpbuildd_134 sbuild_0.65.2-1ubuntu2~ubuntu12.04.1~ppa6 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.7 python-debian_0.1.27ubuntu1~ubuntu12.04.1~ppa2. Syncing the system clock with the buildd NTP service... 23 Dec 23:19:19 ntpdate[11558]: adjust time server 10.211.37.1 offset 0.000059 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8755271', '/home/buildd/filecache-default/bdf524d1fbccc9606fe3cb203c365489d3f7f335'] Unpacking chroot for build PACKAGEBUILD-8755271 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8755271'] Mounting chroot for build PACKAGEBUILD-8755271 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8755271', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8755271 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8755271', 'armhf'] Updating debian chroot for build PACKAGEBUILD-8755271 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main armhf Packages [1436 kB] Get:6 http://ftpmaster.internal xenial/universe armhf Packages [6933 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [848 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4760 kB] Get:9 http://ftpmaster.internal xenial-security/main armhf Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe armhf Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main armhf Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe armhf Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main armhf Packages [137 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe armhf Packages [384 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [74.1 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [246 kB] Fetched 15.4 MB in 19s (808 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'apt-get autoremove' to remove them. The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libisl15 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: advancecomp apt apt-transport-https base-files binutils bsdutils cpp cpp-5 debconf diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libmpfr4 libncurses5 libncursesw5 libp11-kit0 libpng12-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 104 upgraded, 5 newly installed, 1 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 255 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files armhf 9.4ubuntu3 [69.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils armhf 1:2.27.1-1ubuntu3 [48.9 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils armhf 1:3.3-2 [143 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg armhf 1.18.3ubuntu1 [1983 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev armhf 2.21-0ubuntu5 [1585 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin armhf 2.21-0ubuntu5 [58.6 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev armhf 4.3.0-5.16 [798 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 armhf 1:2.24-12 [11.7 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin armhf 2.21-0ubuntu5 [984 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 armhf 5.3.1-4ubuntu1 [49.9 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 armhf 5.3.1-4ubuntu1 [6028 B] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 armhf 5.3.1-4ubuntu1 [244 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base armhf 5.3.1-4ubuntu1 [16.6 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 armhf 1:5.3.1-4ubuntu1 [39.0 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 armhf 5.3.1-4ubuntu1 [88.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 armhf 0.15-3 [399 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 armhf 5.3.1-4ubuntu1 [23.7 MB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 armhf 5.3.1-4ubuntu1 [25.8 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main binutils armhf 2.25.90.20151211-0ubuntu2 [2343 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 armhf 5.3.1-4ubuntu1 [25.3 MB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 armhf 5.3.1-4ubuntu1 [23.9 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev armhf 5.3.1-4ubuntu1 [474 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev armhf 5.3.1-4ubuntu1 [1465 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 armhf 5.3.1-4ubuntu1 [350 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 armhf 2:6.1.0+dfsg-2 [184 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 armhf 3.1.3-2 [169 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libc6 armhf 2.21-0ubuntu5 [3903 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs armhf 1.42.13-1ubuntu1 [177 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs armhf 1.42.13-1ubuntu1 [754 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main findutils armhf 4.4.2-10 [229 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep armhf 2.22-1 [139 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main hostname armhf 3.16ubuntu2 [10.9 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main init armhf 1.24ubuntu2 [3980 B] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 armhf 2.27.1-1ubuntu3 [54.6 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 armhf 2.27.1-1ubuntu3 [14.1 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 armhf 2.27.1-1ubuntu3 [95.3 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 armhf 2.27.1-1ubuntu3 [127 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils armhf 2.88dsf-59.2ubuntu3 [24.5 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main initscripts armhf 2.88dsf-59.2ubuntu3 [24.9 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main util-linux armhf 2.27.1-1ubuntu3 [795 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 armhf 228-2ubuntu2 [50.0 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main udev armhf 228-2ubuntu2 [948 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 armhf 228-2ubuntu2 [180 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main systemd armhf 228-2ubuntu2 [3231 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 armhf 2.4-3 [48.2 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 armhf 6.0+20151024-2ubuntu1 [66.0 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 armhf 6.0+20151024-2ubuntu1 [75.1 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 armhf 6.0+20151024-2ubuntu1 [95.6 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 armhf 2:3.3.10-4ubuntu1 [29.8 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main procps armhf 2:3.3.10-4ubuntu1 [209 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapparmor1 armhf 2.10-0ubuntu9 [25.5 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 armhf 1:2.4.4-4ubuntu1 [33.4 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 armhf 2.27.1-1ubuntu3 [102 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 armhf 2.2.3-2ubuntu3 [28.5 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin armhf 1:2.24-12 [20.1 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main mount armhf 2.27.1-1ubuntu3 [116 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin armhf 6.0+20151024-2ubuntu1 [131 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-modules-5.22 all 5.22.1-2 [2648 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libperl5.22 armhf 5.22.1-2 [2670 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl armhf 5.22.1-2 [237 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-base armhf 5.22.1-2 [1177 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main tar armhf 1.28-2.1 [181 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 armhf 1.1.5 [621 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main apt armhf 1.1.5 [937 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main gpgv armhf 1.4.19-6ubuntu1 [135 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main gnupg armhf 1.4.19-6ubuntu1 [564 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv armhf 228-2ubuntu2 [15.1 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 armhf 3.2.1-4 [16.2 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main libp11-kit0 armhf 0.23.2-2 [91.2 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 armhf 4.7-2 [37.5 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 armhf 3.3.18-1ubuntu1 [459 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libldap-2.4-2 armhf 2.4.41+dfsg-1ubuntu3 [138 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 armhf 1.42.13-1ubuntu1 [64.9 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 armhf 0.198ubuntu1 [5956 B] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 armhf 2:1.02.110-1ubuntu2 [140 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 armhf 1.21-1 [30.0 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 armhf 1.6.4-3 [301 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 armhf 2.4-2 [163 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:85 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 armhf 2.4-3 [69.0 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libss2 armhf 1.42.13-1ubuntu1 [68.4 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support armhf 2.21-0ubuntu5 [7184 B] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 armhf 1.2.54-1 [106 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 armhf 3.9.2-1 [337 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 armhf 1.0.2e-1ubuntu1 [711 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup armhf 2:1.02.110-1ubuntu2 [61.1 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 armhf 1.13.2+dfsg-4 [98.6 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 armhf 1.13.2+dfsg-4 [230 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 armhf 1.13.2+dfsg-4 [26.7 kB] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 armhf 1.13.2+dfsg-4 [77.9 kB] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 armhf 1.5.9-8ubuntu1 [9192 B] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 armhf 1.32-3ubuntu1 [42.2 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls armhf 7.45.0-1ubuntu1 [158 kB] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https armhf 1.1.5 [22.6 kB] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 armhf 1.10.6-1ubuntu1 [141 kB] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main openssl armhf 1.0.2e-1ubuntu1 [486 kB] Get:102 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp armhf 1.20-1 [134 kB] Get:103 http://ftpmaster.internal/ubuntu/ xenial/main cpp armhf 4:5.2.1-16ubuntu2 [27.6 kB] Get:104 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:105 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:106 http://ftpmaster.internal/ubuntu/ xenial/main gcc armhf 4:5.2.1-16ubuntu2 [5242 B] Get:107 http://ftpmaster.internal/ubuntu/ xenial/main g++ armhf 4:5.2.1-16ubuntu2 [1502 B] Get:108 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:109 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 15s (7096 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11455 files and directories currently installed.) Preparing to unpack .../base-files_9.4ubuntu3_armhf.deb ... Unpacking base-files (9.4ubuntu3) over (7.2ubuntu11) ... Setting up base-files (9.4ubuntu3) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... 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Selecting previously unselected package libisl15:armhf. Preparing to unpack .../libisl15_0.15-3_armhf.deb ... Unpacking libisl15:armhf (0.15-3) ... Preparing to unpack .../cpp-5_5.3.1-4ubuntu1_armhf.deb ... Unpacking cpp-5 (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libcc1-0_5.3.1-4ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../binutils_2.25.90.20151211-0ubuntu2_armhf.deb ... Unpacking binutils (2.25.90.20151211-0ubuntu2) over (2.25.1-6ubuntu1) ... Preparing to unpack .../g++-5_5.3.1-4ubuntu1_armhf.deb ... Unpacking g++-5 (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../gcc-5_5.3.1-4ubuntu1_armhf.deb ... Unpacking gcc-5 (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libgcc-5-dev_5.3.1-4ubuntu1_armhf.deb ... Unpacking libgcc-5-dev:armhf (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libstdc++-5-dev_5.3.1-4ubuntu1_armhf.deb ... Unpacking libstdc++-5-dev:armhf (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libstdc++6_5.3.1-4ubuntu1_armhf.deb ... Unpacking libstdc++6:armhf (5.3.1-4ubuntu1) over (5.2.1-22ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libstdc++6:armhf (5.3.1-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11436 files and directories currently installed.) 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11446 files and directories currently installed.) Preparing to unpack .../systemd_228-2ubuntu2_armhf.deb ... Unpacking systemd (228-2ubuntu2) over (225-1ubuntu9) ... Setting up systemd (228-2ubuntu2) ... Installing new version of config file /etc/pam.d/systemd-user ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11447 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_armhf.deb ... Unpacking libselinux1:armhf (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:armhf (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11447 files and directories currently installed.) Preparing to unpack .../libtinfo5_6.0+20151024-2ubuntu1_armhf.deb ... Unpacking libtinfo5:armhf (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libtinfo5:armhf (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11447 files and directories currently installed.) Preparing to unpack .../libncurses5_6.0+20151024-2ubuntu1_armhf.deb ... Unpacking libncurses5:armhf (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:armhf (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Unpacking libapparmor1:armhf (2.10-0ubuntu9) over (2.10-0ubuntu6) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapparmor1:armhf (2.10-0ubuntu9) ... Processing triggers for systemd (228-2ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11456 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.4-4ubuntu1_all.deb ... Unpacking libaudit-common (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.4-4ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11456 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.4.4-4ubuntu1_armhf.deb ... Unpacking libaudit1:armhf (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libaudit1:armhf (1:2.4.4-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11456 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_armhf.deb ... Unpacking libmount1:armhf (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:armhf (2.27.1-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12057 files and directories currently installed.) Preparing to unpack .../gpgv_1.4.19-6ubuntu1_armhf.deb ... Unpacking gpgv (1.4.19-6ubuntu1) over (1.4.18-7ubuntu1) ... Setting up gpgv (1.4.19-6ubuntu1) ... (Reading database ... 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Unpacking libdpkg-perl (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Preparing to unpack .../gcc_4%3a5.2.1-16ubuntu2_armhf.deb ... Removing old gcc doc directory. Unpacking gcc (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../g++_4%3a5.2.1-16ubuntu2_armhf.deb ... Unpacking g++ (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../pkg-create-dbgsym_0.70_all.deb ... Unpacking pkg-create-dbgsym (0.70) over (0.69) ... Preparing to unpack .../pkgbinarymangler_125_all.deb ... Unpacking pkgbinarymangler (125) over (122) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libc-dev-bin (2.21-0ubuntu5) ... Setting up linux-libc-dev:armhf (4.3.0-5.16) ... Setting up libc6-dev:armhf (2.21-0ubuntu5) ... Setting up libgomp1:armhf (5.3.1-4ubuntu1) ... Setting up libatomic1:armhf (5.3.1-4ubuntu1) ... Setting up libasan2:armhf (5.3.1-4ubuntu1) ... Setting up libubsan0:armhf (5.3.1-4ubuntu1) ... Setting up libgmp10:armhf (2:6.1.0+dfsg-2) ... Setting up libisl15:armhf (0.15-3) ... Setting up libmpfr4:armhf (3.1.3-2) ... Setting up cpp-5 (5.3.1-4ubuntu1) ... Setting up libcc1-0:armhf (5.3.1-4ubuntu1) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgcc-5-dev:armhf (5.3.1-4ubuntu1) ... Setting up gcc-5 (5.3.1-4ubuntu1) ... Setting up libstdc++-5-dev:armhf (5.3.1-4ubuntu1) ... Setting up g++-5 (5.3.1-4ubuntu1) ... Setting up libprocps4:armhf (2:3.3.10-4ubuntu1) ... Setting up procps (2:3.3.10-4ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up udev (228-2ubuntu2) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up perl-modules-5.22 (5.22.1-2) ... Setting up libperl5.22:armhf (5.22.1-2) ... Setting up perl (5.22.1-2) ... Setting up apt (1.1.5) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libffi6:armhf (3.2.1-4) ... Setting up libp11-kit0:armhf (0.23.2-2) ... Setting up libtasn1-6:armhf (4.7-2) ... Setting up libgnutls-deb0-28:armhf (3.3.18-1ubuntu1) ... Setting up libldap-2.4-2:armhf (2.4.41+dfsg-1ubuntu3) ... Setting up libpng12-0:armhf (1.2.54-1) ... Setting up libsqlite3-0:armhf (3.9.2-1) ... Setting up libssl1.0.0:armhf (1.0.2e-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libkrb5support0:armhf (1.13.2+dfsg-4) ... Setting up libk5crypto3:armhf (1.13.2+dfsg-4) ... Setting up libkeyutils1:armhf (1.5.9-8ubuntu1) ... Setting up libkrb5-3:armhf (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-4) ... Setting up libidn11:armhf (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:armhf (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.5) ... Setting up libdbus-1-3:armhf (1.10.6-1ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... Setting up pkgbinarymangler (125) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8755271', 'armhf', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=xenial-proposed', '--purge=never', '--nolog', 't-coffee_11.00.8cbe486-2.dsc'] Initiating build PACKAGEBUILD-8755271 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.2.0-95-highbank #135-Ubuntu SMP PREEMPT Tue Nov 10 14:26:08 UTC 2015 armv7l sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on kishi10.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ t-coffee 11.00.8cbe486-2 (armhf) 23 Dec 2015 23:23 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: t-coffee Version: 11.00.8cbe486-2 Source Version: 11.00.8cbe486-2 Distribution: xenial-proposed Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/t-coffee-yrbASO/t-coffee-11.00.8cbe486' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/t-coffee-yrbASO' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8755271/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── t-coffee_11.00.8cbe486-2.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-qT7kQ8/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Packages [529 B] Ign:4 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Packages [529 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-qT7kQ8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12053 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9) Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9) dpkg-deb: building package 'sbuild-build-depends-t-coffee-dummy' in '/«BUILDDIR»/resolver-h7TBLJ/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Sources [422 B] Get:5 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Packages [686 B] Ign:4 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Sources [422 B] Get:5 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Packages [686 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install t-coffee build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-t-coffee-dummy 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 13.8 MB/13.8 MB of archives. After this operation, 51.7 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-t-coffee-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-h7TBLJ/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [926 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main armhf groff-base armhf 1.22.3-4 [1030 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main armhf bsdmainutils armhf 9.0.6ubuntu1 [169 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main armhf libpipeline1 armhf 1.4.1-1 [21.0 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main armhf man-db armhf 2.7.5-1 [836 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main armhf libunistring0 armhf 0.9.3-5.2ubuntu1 [250 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main armhf libmagic1 armhf 1:5.25-2ubuntu1 [211 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main armhf file armhf 1:5.25-2ubuntu1 [20.9 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main armhf libasprintf0v5 armhf 0.19.6-1ubuntu1 [6666 B] Get:10 http://ftpmaster.internal/ubuntu xenial/main armhf gettext-base armhf 0.19.6-1ubuntu1 [45.1 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main armhf libglib2.0-0 armhf 2.47.3-3 [975 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main armhf libicu55 armhf 55.1-6ubuntu1 [7413 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main armhf libxml2 armhf 2.9.2+zdfsg1-4ubuntu2 [602 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main armhf libcroco3 armhf 0.6.11-1 [70.0 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main armhf gettext armhf 0.19.6-1ubuntu1 [1008 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main armhf po-debconf all 1.0.18 [234 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main armhf libarchive-zip-perl all 1.53-1 [87.0 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main armhf dh-strip-nondeterminism all 0.014-1 [5596 B] Get:22 http://ftpmaster.internal/ubuntu xenial/main armhf debhelper all 9.20151126ubuntu1 [741 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.8 MB in 0s (15.8 MB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12053 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-4_armhf.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_armhf.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../libpipeline1_1.4.1-1_armhf.deb ... Unpacking libpipeline1:armhf (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_armhf.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:armhf. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_armhf.deb ... Unpacking libunistring0:armhf (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_armhf.deb ... Unpacking libmagic1:armhf (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_armhf.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package libasprintf0v5:armhf. Preparing to unpack .../libasprintf0v5_0.19.6-1ubuntu1_armhf.deb ... Unpacking libasprintf0v5:armhf (0.19.6-1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.6-1ubuntu1_armhf.deb ... Unpacking gettext-base (0.19.6-1ubuntu1) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../libglib2.0-0_2.47.3-3_armhf.deb ... Unpacking libglib2.0-0:armhf (2.47.3-3) ... Selecting previously unselected package libicu55:armhf. Preparing to unpack .../libicu55_55.1-6ubuntu1_armhf.deb ... Unpacking libicu55:armhf (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu2_armhf.deb ... Unpacking libxml2:armhf (2.9.2+zdfsg1-4ubuntu2) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ... Unpacking libcroco3:armhf (0.6.11-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.6-1ubuntu1_armhf.deb ... Unpacking gettext (0.19.6-1ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.18_all.deb ... Unpacking po-debconf (1.0.18) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ... Unpacking libarchive-zip-perl (1.53-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.014-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ... Unpacking dh-strip-nondeterminism (0.014-1) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20151126ubuntu1_all.deb ... Unpacking debhelper (9.20151126ubuntu1) ... Selecting previously unselected package sbuild-build-depends-t-coffee-dummy. Preparing to unpack .../sbuild-build-depends-t-coffee-dummy.deb ... Unpacking sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up groff-base (1.22.3-4) ... Setting up bsdmainutils (9.0.6ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpipeline1:armhf (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:armhf (0.9.3-5.2ubuntu1) ... Setting up libmagic1:armhf (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:armhf (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:armhf (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:armhf (55.1-6ubuntu1) ... Setting up libxml2:armhf (2.9.2+zdfsg1-4ubuntu2) ... Setting up libcroco3:armhf (0.6.11-1) ... Setting up gettext (0.19.6-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.53-1) ... Setting up libfile-stripnondeterminism-perl (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up dh-strip-nondeterminism (0.014-1) ... Setting up debhelper (9.20151126ubuntu1) ... Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-95-highbank armhf (armv7l) Toolchain package versions: binutils_2.25.90.20151211-0ubuntu2 dpkg-dev_1.18.3ubuntu1 g++-5_5.3.1-4ubuntu1 gcc-5_5.3.1-4ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-4ubuntu1 libstdc++6_5.3.1-4ubuntu1 linux-libc-dev_4.3.0-5.16 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.5 apt-transport-https_1.1.5 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.90.20151211-0ubuntu2 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.3.1-4ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1ubuntu2 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 g++_4:5.2.1-16ubuntu2 g++-5_5.3.1-4ubuntu1 gcc_4:5.2.1-16ubuntu2 gcc-5_5.3.1-4ubuntu1 gcc-5-base_5.3.1-4ubuntu1 gettext_0.19.6-1ubuntu1 gettext-base_0.19.6-1ubuntu1 gnupg_1.4.19-6ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu9 libapt-pkg4.16_1.0.10.2ubuntu1 libapt-pkg5.0_1.1.5 libarchive-zip-perl_1.53-1 libasan2_5.3.1-4ubuntu1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.6-1ubuntu1 libatomic1_5.3.1-4ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu5 libc-dev-bin_2.21-0ubuntu5 libc6_2.21-0ubuntu5 libc6-dev_2.21-0ubuntu5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-4ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu1 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu2 libdpkg-perl_1.18.3ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.3.1-4ubuntu1 libgcc1_1:5.3.1-4ubuntu1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.3-3 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.3.1-4ubuntu1 libgpg-error0_1.21-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libisl15_0.15-3 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu3 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4ubuntu27 libnih1_1.0.3-4ubuntu27 libp11-kit0_0.23.2-2 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libperl5.22_5.22.1-2 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libprocps4_2:3.3.10-4ubuntu1 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2e-1ubuntu1 libstdc++-5-dev_5.3.1-4ubuntu1 libstdc++6_5.3.1-4ubuntu1 libsystemd0_228-2ubuntu2 libtasn1-6_4.7-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2ubuntu1 libubsan0_5.3.1-4ubuntu1 libudev1_228-2ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4ubuntu2 linux-libc-dev_4.3.0-5.16 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu5 ncurses-base_6.0+20151024-2ubuntu1 ncurses-bin_6.0+20151024-2ubuntu1 openssl_1.0.2e-1ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.22.1-2 perl-base_5.22.1-2 perl-modules-5.22_5.22.1-2 pkg-create-dbgsym_0.70 pkgbinarymangler_125 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu1 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-t-coffee-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-2ubuntu2 systemd-sysv_228-2ubuntu2 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-2ubuntu2 util-linux_2.27.1-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Wed Dec 23 08:19:33 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./t-coffee_11.00.8cbe486-2.dsc dpkg-source: info: extracting t-coffee in t-coffee-11.00.8cbe486 dpkg-source: info: unpacking t-coffee_11.00.8cbe486.orig.tar.gz dpkg-source: info: unpacking t-coffee_11.00.8cbe486-2.debian.tar.xz dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LANGUAGE=en_GB: LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package t-coffee dpkg-buildpackage: source version 11.00.8cbe486-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build t-coffee-11.00.8cbe486 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source dh_testdir -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/«PKGBUILDDIR»' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --sourcedirectory=t_coffee_source dh_testdir -a -O--sourcedirectory=t_coffee_source dh_auto_configure -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_build -- -i USER_BIN=../bin/ FCC="gfortran -g -O2 -fstack-protector-strong" all make -j1 -i USER_BIN=../bin/ "FCC=gfortran -g -O2 -fstack-protector-strong" all make[2]: Entering directory '/«PKGBUILDDIR»/t_coffee_source' CC km_coffee/kmeans.c CC km_coffee/km_coffee.c km_coffee/km_coffee.c: In function 'void traverse_km_tree(KM_node*, int*, const SeqSet*, char*, int, int, int, char*)': km_coffee/km_coffee.c:148:39: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command, "%li",current->id); ^ km_coffee/km_coffee.c:157:209: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); ^ km_coffee/km_coffee.c:157:209: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=] km_coffee/km_coffee.c:159:201: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); ^ km_coffee/km_coffee.c:169:39: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command, "%li",current->id); ^ km_coffee/km_coffee.c:172:209: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); ^ km_coffee/km_coffee.c:172:209: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=] km_coffee/km_coffee.c:174:201: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); ^ km_coffee/km_coffee.c:185:42: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command, "%li.fa",current->id); ^ km_coffee/km_coffee.c:195:169: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=] sprintf(command, "t_coffee -output fasta_aln -method %s -quiet -outfile %li.fa -n_core %i -gapopen %i -profile FILE::prf.fa ", method, current->id,n_cores, gapopen); ^ km_coffee/km_coffee.c:201:57: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(prf_F, "%li.fa\n", current->children[j]->id); ^ km_coffee/km_coffee.c: In function 'int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)': km_coffee/km_coffee.c:491:19: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ^ CC km_coffee/km_util.c km_coffee/km_util.c: In function 'void* my_malloc(size_t)': km_coffee/km_util.c:49:72: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); ^ km_coffee/km_util.c: In function 'void* my_calloc(size_t, size_t)': km_coffee/km_util.c:61:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); ^ km_coffee/km_util.c: In function 'void* my_realloc(void*, size_t)': km_coffee/km_util.c:74:72: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); ^ km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': km_coffee/km_util.c:96:70: warning: format '%s' expects a matching 'char*' argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ^ CC km_coffee/classes.c CC km_coffee/Stack.c CC km_coffee/Vector.c CC io_lib/io_func.c io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] if (!A)return NULL; ^ io_lib/io_func.c: In function 'int** read_matrice(char*)': io_lib/io_func.c:511:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ^ io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': io_lib/io_func.c:971:115: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ^ CC io_lib/tree_util.c io_lib/tree_util.c: In function 'tnode* tree_scan(Alignment*, NT_node, char*, char*)': io_lib/tree_util.c:836:43: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^ io_lib/tree_util.c: In function 'FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)': io_lib/tree_util.c:2803:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&dist); ^ io_lib/tree_util.c:2811:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&bootstrap); ^ CC io_lib/pb_util_read_sequence.c io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': io_lib/pb_util_read_sequence.c:144:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ^ io_lib/pb_util_read_sequence.c:149:50: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for(i=1;iA)=aln2bootstrap (D1->A, ATOI_ACTION (1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:10958:32: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); ^ util_lib/reformat.c:11157:36: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(2))D=atof (ACTION(2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11183:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11282:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11283:34: note: in expansion of macro 'ATOI_ACTION' treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11290:38: note: in expansion of macro 'ATOI_ACTION' else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11297:35: note: in expansion of macro 'ATOI_ACTION' D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); ^ util_lib/reformat.c:11325:27: warning: null argument where non-null required (argument 1) [-Wnonnull] ng=atoi(ACTION (2))+1; ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11444:44: note: in expansion of macro 'ATOI_ACTION' D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); ^ util_lib/reformat.c:11530:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11531:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:11539:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11540:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11669:37: note: in expansion of macro 'ATOI_ACTION' D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^ util_lib/reformat.c:12301:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12308:10: note: in expansion of macro 'ATOI_ACTION' F->t=ATOI_ACTION(2); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12309:10: note: in expansion of macro 'ATOI_ACTION' F->f=ATOI_ACTION(3); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12310:11: note: in expansion of macro 'ATOI_ACTION' F->p1=ATOI_ACTION(4); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12311:11: note: in expansion of macro 'ATOI_ACTION' F->p2=ATOI_ACTION(5); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12312:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(6); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12313:11: note: in expansion of macro 'ATOI_ACTION' F->p3=ATOI_ACTION(7); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12336:34: note: in expansion of macro 'ATOI_ACTION' D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12476:10: note: in expansion of macro 'ATOI_ACTION' if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12477:19: note: in expansion of macro 'ATOI_ACTION' km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12481:27: note: in expansion of macro 'ATOI_ACTION' D1->A=gap_trim (D1->A,ATOI_ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12488:34: note: in expansion of macro 'ATOI_ACTION' D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13008:7: note: in expansion of macro 'ATOI_ACTION' t=ATOI_ACTION(1); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13009:7: note: in expansion of macro 'ATOI_ACTION' f=ATOI_ACTION(2); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13010:8: note: in expansion of macro 'ATOI_ACTION' p1=ATOI_ACTION(3); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13011:8: note: in expansion of macro 'ATOI_ACTION' p2=ATOI_ACTION(4); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13012:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1502:34: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d", &result); ^ util_lib/reformat.c: In function 'char* get_pdb_id(char*)': util_lib/reformat.c:1540:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ^ util_lib/reformat.c: In function 'int format_is_msf(char*)': util_lib/reformat.c:2092:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp , "%s", buf); ^ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3590:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^ util_lib/reformat.c:3597:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^ util_lib/reformat.c:3606:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^ util_lib/reformat.c:3612:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ^ util_lib/reformat.c:3614:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ^ util_lib/reformat.c:3625:21: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ^ util_lib/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:3898:46: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ^ util_lib/reformat.c:3901:105: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); ^ util_lib/reformat.c: In function 'Sequence* get_struc_gor(char*)': util_lib/reformat.c:4098:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ^ util_lib/reformat.c:4119:63: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ^ util_lib/reformat.c:4124:66: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ^ util_lib/reformat.c: In function 'Sequence* get_sequence_dali(char*)': util_lib/reformat.c:4161:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s",name); ^ util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4236:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ^ util_lib/reformat.c: In function 'Sequence* get_swissprot_sequence(char*, char*)': util_lib/reformat.c:5281:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (buf, LONG_STRING, fp); ^ util_lib/reformat.c:5300:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (buf, LONG_STRING, fp); ^ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5319:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ^ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:5672:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ^ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:5721:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^ util_lib/reformat.c:5743:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^ util_lib/reformat.c: In function 'float output_maln_pval(char*, Alignment*)': util_lib/reformat.c:5941:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",string); ^ util_lib/reformat.c: In function 'Alignment* similarities_file2aln(char*)': util_lib/reformat.c:6106:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ^ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:13557:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ^ util_lib/reformat.c:13570:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ^ util_lib/reformat.c:13595:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:13620:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^ util_lib/reformat.c:13637:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ^ util_lib/reformat.c:13650:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ^ util_lib/reformat.c:13677:22: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^ util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': util_lib/reformat.c:13788:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^ CC util_lib/util_make_tree.c CC util_lib/util_domain_constraints_list.c CC util_lib/aln_convertion_util.c util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': util_lib/aln_convertion_util.c:7269:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^ util_lib/aln_convertion_util.c:7288:59: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ^ util_lib/aln_convertion_util.c:7292:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^ CC util_lib/util.c util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': util_lib/util.c:281:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ^ util_lib/util.c:286:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ^ util_lib/util.c:289:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ^ util_lib/util.c:306:36: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j, size, len, fp); ^ util_lib/util.c:311:34: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread (ra_j_1, size, len, fp); ^ util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': util_lib/util.c:420:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( key2, el_size, entry_len,fp); ^ util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': util_lib/util.c:847:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ^ util_lib/util.c: In function 'int quantile(int, char**)': util_lib/util.c:906:38: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ^ util_lib/util.c: In function 'int** input_array_int(char*)': util_lib/util.c:1262:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &len); ^ util_lib/util.c:1266:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &len2); ^ util_lib/util.c:1269:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ^ util_lib/util.c:1270:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ^ util_lib/util.c: In function 'int perl_strstr(char*, char*)': util_lib/util.c:1925:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); ^ util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': util_lib/util.c:5090:34: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",list[n]); ^ util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': util_lib/util.c:6571:22: warning: second parameter of 'va_start' not last named argument [-Wvarargs] va_start (ap, usage); ^ util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:6838:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^ util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': util_lib/util.c:6858:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", string); ^ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:7214:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ^ util_lib/util.c:7244:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ^ util_lib/util.c: In function 'int check_for_update(char*)': util_lib/util.c:7331:43: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ^ CC util_lib/reformat_struc.c util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': util_lib/reformat_struc.c:326:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^ util_lib/reformat_struc.c:328:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^ util_lib/reformat_struc.c:334:69: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ^ util_lib/reformat_struc.c:361:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^ util_lib/reformat_struc.c:363:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ^ util_lib/reformat_struc.c:372:100: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); ^ CC util_lib/util_job_handling.c CC util_lib/util_constraints_list.c util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': util_lib/util_constraints_list.c:2163:81: warning: too many arguments for format [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ^ util_lib/util_constraints_list.c: In function 'Constraint_list* read_constraint_list_file(Constraint_list*, char*)': util_lib/util_constraints_list.c:2775:76: warning: too many arguments for format [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ^ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:577:18: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (tdir); ^ util_lib/util_constraints_list.c:580:18: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^ util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': util_lib/util_constraints_list.c:1140:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ^ util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': util_lib/util_constraints_list.c:1182:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ^ util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': util_lib/util_constraints_list.c:2525:42: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ^ util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': util_lib/util_constraints_list.c:2833:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ^ util_lib/util_constraints_list.c:2838:34: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ^ util_lib/util_constraints_list.c:2870:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ^ util_lib/util_constraints_list.c:2895:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line , 200 , fp); ^ util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': util_lib/util_constraints_list.c:3903:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ^ CC util_lib/util_aln_analyze.c CC util_lib/random.c CC util_lib/util_dps.c CC util_lib/hsearch.c CC util_lib/aln_compare.c CC util_lib/util_declare.c Linking... dp_lib/util_dp_drivers.o: In function `hh_pair(TC_method*, char*, Constraint_list*)': /«PKGBUILDDIR»/t_coffee_source/dp_lib/util_dp_drivers.c:1048: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/«PKGBUILDDIR»/t_coffee_source' make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_test -a -O--sourcedirectory=t_coffee_source fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_installdocs -a -O--sourcedirectory=t_coffee_source dh_installchangelogs -a -O--sourcedirectory=t_coffee_source dh_installman -a -O--sourcedirectory=t_coffee_source dh_perl -a -O--sourcedirectory=t_coffee_source dh_link -a -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/«PKGBUILDDIR»' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory '/«PKGBUILDDIR»' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: t-coffee dh_strip debug symbol extraction: packages to act on: t-coffee dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dpkg-shlibdeps: warning: debian/t-coffee/usr/bin/t_coffee contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/t-coffee/usr/bin/t_coffee was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols) dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform armhf: t-coffee dh_gencontrol debug symbol wrapper: packages to act on: t-coffee dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package t-coffee (pkgdir debian/t-coffee, ddeb package dir debian/t-coffee-dbgsym) dh_gencontrol debug symbol wrapper: building t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--sourcedirectory=t_coffee_source dh_builddeb -a -O--sourcedirectory=t_coffee_source INFO: pkgstriptranslations version 125 pkgstriptranslations: processing t-coffee (in debian/t-coffee); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/t-coffee/DEBIAN/control, package t-coffee, directory debian/t-coffee DEBUG: wait t-coffee 1:t-coffee DEBUG: clear t-coffee 1:t-coffee DEBUG: done t-coffee pkgstripfiles: Truncating usr/share/doc/t-coffee/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package t-coffee ... pkgstripfiles: No PNG files. dpkg-deb: building package 't-coffee' in '../t-coffee_11.00.8cbe486-2_armhf.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../t-coffee_11.00.8cbe486-2_armhf.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build t-coffee-11.00.8cbe486 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151223-2330 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ t-coffee_11.00.8cbe486-2_armhf.changes: ─────────────────────────────────────── Format: 1.8 Date: Tue, 22 Dec 2015 19:02:14 +0100 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: armhf Version: 11.00.8cbe486-2 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 631249 751579 Changes: t-coffee (11.00.8cbe486-2) unstable; urgency=medium . * cme fix dpkg-control * update debian/copyright * fix clean target * compress changelog with '-n' option * propagate hardening options * Do not build unused TMalign * When creating subdirectories in $HOME do not make these world writable but keep users umask Closes: #751579 * Drop redundant debian/README.source * Package builds for all architectures so this Closes: #631249 (feel free to reopen if tests might keep on failing on armel) Checksums-Sha1: 5e8a8e4ebb340db864a3a36e7f4a51ee09dc96f5 1519162 t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb d18164c6072f8d2a358ad2a64fd7104a3c8c8e40 751060 t-coffee_11.00.8cbe486-2_armhf.deb Checksums-Sha256: 74184729c191328158d8761a0f1943a848b7528b07ccc8490ef832b9d0672196 1519162 t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb d56cb4f1f6280ab465b458985734f180e34bd2a93edfee35639c6f94084b5f06 751060 t-coffee_11.00.8cbe486-2_armhf.deb Files: 363bb7624e228e85a5e875fe4a3c9862 1519162 science extra t-coffee-dbgsym_11.00.8cbe486-2_armhf.ddeb b97b786fbd4088fa1f1e13cdea61cdd6 751060 science optional t-coffee_11.00.8cbe486-2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ t-coffee_11.00.8cbe486-2_armhf.deb ────────────────────────────────── new debian package, version 2.0. size 751060 bytes: control archive= 1295 bytes. 1680 bytes, 30 lines control 333 bytes, 5 lines md5sums Package: t-coffee Version: 11.00.8cbe486-2 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1734 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 4.3.0) Recommends: amap-align, clustalo, clustalw, dialign-tx, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples, fsa Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. drwxr-xr-x root/root 0 2015-12-23 23:29 ./ drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/ drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/bin/ -rwxr-xr-x root/root 1757044 2015-12-23 23:29 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/share/ drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2013-09-12 08:59 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 1757 2015-12-23 23:30 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1432 2015-12-21 20:58 ./usr/share/doc/t-coffee/copyright drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-23 23:29 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2015-12-23 23:29 ./usr/share/man/man1/t_coffee.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 37924 Build-Time: 370 Distribution: xenial-proposed Host Architecture: armhf Install-Time: 45 Job: t-coffee_11.00.8cbe486-2.dsc Machine Architecture: armhf Package: t-coffee Package-Time: 421 Source-Version: 11.00.8cbe486-2 Space: 37924 Status: successful Version: 11.00.8cbe486-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151223-2330 Build needed 00:07:01, 37924k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8755271'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8755271/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8755271'] Unmounting chroot for build PACKAGEBUILD-8755271... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8755271'] Removing build PACKAGEBUILD-8755271