RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kishi12 3.2.0-54-highbank #82-Ubuntu SMP PREEMPT Tue Sep 10 20:59:15 UTC 2013 armv7l Buildd toolchain package versions: launchpad-buildd_119~0.IS.08.04 python-lpbuildd_119~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 27 Nov 17:09:39 ntpdate[23646]: adjust time server 10.211.37.1 offset -0.000163 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5274657', '/home/buildd/filecache-default/b2610aaa6cbeb34c5842e3f132a84dda2bfe287e'] Unpacking chroot for build PACKAGEBUILD-5274657 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5274657'] Mounting chroot for build PACKAGEBUILD-5274657 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5274657', 'deb http://ftpmaster.internal/ubuntu trusty main universe', 'deb http://ftpmaster.internal/ubuntu trusty-security main universe', 'deb http://ftpmaster.internal/ubuntu trusty-updates main universe', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-5274657 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5274657', 'armhf'] Updating debian chroot for build PACKAGEBUILD-5274657 Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty-updates InRelease Get:1 http://archive-team.internal trusty Release [730 B] Ign http://ftpmaster.internal trusty-proposed InRelease Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:4 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal trusty Release [49.6 kB] Get:7 http://archive-team.internal trusty/main armhf Packages Get:8 http://ftpmaster.internal trusty-security Release [49.6 kB] Get:9 http://ftpmaster.internal trusty-updates Release [49.6 kB] Ign http://archive-team.internal trusty/main Translation-en Get:10 http://ftpmaster.internal trusty-proposed Release [49.6 kB] Get:11 http://ftpmaster.internal trusty/main armhf Packages [1241 kB] Get:12 http://ftpmaster.internal trusty/universe armhf Packages [5609 kB] Get:13 http://ftpmaster.internal trusty/main Translation-en [728 kB] Get:14 http://ftpmaster.internal trusty/universe Translation-en [3971 kB] Get:15 http://ftpmaster.internal trusty-security/main armhf Packages [14 B] Get:16 http://ftpmaster.internal trusty-security/universe armhf Packages [14 B] Get:17 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal trusty-updates/main armhf Packages [14 B] Get:20 http://ftpmaster.internal trusty-updates/universe armhf Packages [14 B] Get:21 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal trusty-proposed/main armhf Packages [55.5 kB] Get:24 http://ftpmaster.internal trusty-proposed/universe armhf Packages [239 kB] Get:25 http://ftpmaster.internal trusty-proposed/main Translation-en [31.9 kB] Get:26 http://ftpmaster.internal trusty-proposed/universe Translation-en [141 kB] Fetched 12.2 MB in 15s (803 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libdb5.3 libffi6 libprocps1 The following packages will be upgraded: adduser advancecomp apt apt-transport-https base-files base-passwd binutils build-essential busybox-initramfs bzip2 coreutils cpp-4.8 debconf diffutils dpkg dpkg-dev findutils g++-4.8 gcc-4.8 gcc-4.8-base gnupg gpgv grep ifupdown initramfs-tools initramfs-tools-bin iproute iproute2 kmod libapt-pkg4.12 libasan0 libasn1-8-heimdal libatomic1 libbz2-1.0 libcloog-isl4 libcurl3-gnutls libdbus-1-3 libdpkg-perl libdrm2 libgcc-4.8-dev libgcc1 libgmp10 libgomp1 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libisl10 libjson-c2 libjson0 libk5crypto3 libkeyutils1 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libmpc3 libmpfr4 libnih-dbus1 libnih1 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libplymouth2 libpng12-0 libroken18-heimdal libsasl2-2 libsasl2-modules libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libsqlite3-0 libstdc++-4.8-dev libstdc++6 libudev1 libusb-0.1-4 libwind0-heimdal linux-libc-dev module-init-tools patch perl perl-base perl-modules plymouth procps sed tar udev upstart 96 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 42.3 MB of archives. After this operation, 3484 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! base-files coreutils diffutils dpkg findutils grep libdb5.3 perl perl-base perl-modules bzip2 libbz2-1.0 sed tar libgomp1 libasan0 gcc-4.8-base libgcc1 libatomic1 libmpfr4 cpp-4.8 binutils libstdc++-4.8-dev g++-4.8 gcc-4.8 libgcc-4.8-dev libstdc++6 libgmp10 libcloog-isl4 libisl10 libmpc3 libapt-pkg4.12 libusb-0.1-4 gpgv gnupg apt base-passwd debconf libpam0g libselinux1 libpam-modules-bin libpam-modules libsemanage-common libsemanage1 libsepol1 libffi6 libp11-kit0 libsqlite3-0 libdbus-1-3 libdrm2 libjson-c2 libkmod2 libnih-dbus1 libnih1 udev libudev1 libprocps1 procps initramfs-tools initramfs-tools-bin busybox-initramfs kmod module-init-tools plymouth libpng12-0 libplymouth2 libroken18-heimdal libasn1-8-heimdal libkeyutils1 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libhcrypto4-heimdal libheimbase1-heimdal libwind0-heimdal libhx509-5-heimdal libkrb5-26-heimdal libheimntlm0-heimdal libgssapi3-heimdal libsasl2-modules-db libsasl2-2 libldap-2.4-2 libcurl3-gnutls libpam-runtime adduser iproute2 ifupdown libjson0 upstart apt-transport-https libsasl2-modules advancecomp dpkg-dev libdpkg-perl patch build-essential iproute linux-libc-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ trusty/main base-files armhf 6.12ubuntu5 [69.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty/main coreutils armhf 8.21-1ubuntu3 [1968 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty/main diffutils armhf 1:3.3-1 [180 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main dpkg armhf 1.17.1ubuntu1 [1937 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main findutils armhf 4.4.2-6ubuntu2 [223 kB] Get:6 http://ftpmaster.internal/ubuntu/ trusty/main grep armhf 2.15-1 [141 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libdb5.3 armhf 5.3.28-3 [672 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main perl armhf 5.18.1-4build1 [3664 kB] Get:9 http://ftpmaster.internal/ubuntu/ trusty/main perl-base armhf 5.18.1-4build1 [1450 kB] Get:10 http://ftpmaster.internal/ubuntu/ trusty/main perl-modules all 5.18.1-4build1 [3921 kB] Get:11 http://ftpmaster.internal/ubuntu/ trusty/main bzip2 armhf 1.0.6-5 [36.6 kB] Get:12 http://ftpmaster.internal/ubuntu/ trusty/main libbz2-1.0 armhf 1.0.6-5 [33.5 kB] Get:13 http://ftpmaster.internal/ubuntu/ trusty/main sed armhf 4.2.2-2ubuntu1 [136 kB] Get:14 http://ftpmaster.internal/ubuntu/ trusty/main tar armhf 1.27-3 [200 kB] Get:15 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgomp1 armhf 4.8.2-5ubuntu3 [22.2 kB] Get:16 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libasan0 armhf 4.8.2-5ubuntu3 [56.9 kB] Get:17 http://ftpmaster.internal/ubuntu/ trusty-proposed/main gcc-4.8-base armhf 4.8.2-5ubuntu3 [14.1 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgcc1 armhf 1:4.8.2-5ubuntu3 [40.5 kB] Get:19 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libatomic1 armhf 4.8.2-5ubuntu3 [6044 B] Get:20 http://ftpmaster.internal/ubuntu/ trusty/main libmpfr4 armhf 3.1.2-1 [184 kB] Get:21 http://ftpmaster.internal/ubuntu/ trusty-proposed/main cpp-4.8 armhf 4.8.2-5ubuntu3 [3970 kB] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main binutils armhf 2.23.91.20131123-1ubuntu1 [2003 kB] Get:23 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libstdc++-4.8-dev armhf 4.8.2-5ubuntu3 [1074 kB] Get:24 http://ftpmaster.internal/ubuntu/ trusty-proposed/main g++-4.8 armhf 4.8.2-5ubuntu3 [4286 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty-proposed/main gcc-4.8 armhf 4.8.2-5ubuntu3 [4363 kB] Get:26 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgcc-4.8-dev armhf 4.8.2-5ubuntu3 [209 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libstdc++6 armhf 4.8.2-5ubuntu3 [222 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libgmp10 armhf 2:5.1.2+dfsg-3ubuntu2 [187 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main libcloog-isl4 armhf 0.18.1-3 [47.1 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main libisl10 armhf 0.12.1-2 [324 kB] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main libmpc3 armhf 1.0.1-1ubuntu1 [30.6 kB] Get:32 http://ftpmaster.internal/ubuntu/ trusty/main libapt-pkg4.12 armhf 0.9.13~exp1ubuntu3 [584 kB] Get:33 http://ftpmaster.internal/ubuntu/ trusty/main libusb-0.1-4 armhf 2:0.1.12-23.3 [14.6 kB] Get:34 http://ftpmaster.internal/ubuntu/ trusty/main gpgv armhf 1.4.15-1.1ubuntu1 [150 kB] Get:35 http://ftpmaster.internal/ubuntu/ trusty/main gnupg armhf 1.4.15-1.1ubuntu1 [690 kB] Get:36 http://ftpmaster.internal/ubuntu/ trusty/main apt armhf 0.9.13~exp1ubuntu3 [932 kB] Get:37 http://ftpmaster.internal/ubuntu/ trusty/main base-passwd armhf 3.5.28 [37.7 kB] Get:38 http://ftpmaster.internal/ubuntu/ trusty/main debconf all 1.5.51ubuntu1 [148 kB] Get:39 http://ftpmaster.internal/ubuntu/ trusty/main libpam0g armhf 1.1.3-10ubuntu1 [54.5 kB] Get:40 http://ftpmaster.internal/ubuntu/ trusty/main libselinux1 armhf 2.2.1-1ubuntu1 [56.9 kB] Get:41 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules-bin armhf 1.1.3-10ubuntu1 [41.3 kB] Get:42 http://ftpmaster.internal/ubuntu/ trusty/main libpam-modules armhf 1.1.3-10ubuntu1 [251 kB] Get:43 http://ftpmaster.internal/ubuntu/ trusty/main libsemanage-common all 2.2-1 [6488 B] Get:44 http://ftpmaster.internal/ubuntu/ trusty/main libsemanage1 armhf 2.2-1 [69.3 kB] Get:45 http://ftpmaster.internal/ubuntu/ trusty/main libsepol1 armhf 2.2-1 [113 kB] Get:46 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libffi6 armhf 3.0.13-8 [15.0 kB] Get:47 http://ftpmaster.internal/ubuntu/ trusty/main libp11-kit0 armhf 0.20.1-2ubuntu1 [78.7 kB] Get:48 http://ftpmaster.internal/ubuntu/ trusty/main libsqlite3-0 armhf 3.8.1-1ubuntu1 [324 kB] Get:49 http://ftpmaster.internal/ubuntu/ trusty/main libdbus-1-3 armhf 1.6.18-0ubuntu2 [111 kB] Get:50 http://ftpmaster.internal/ubuntu/ trusty/main libdrm2 armhf 2.4.49-2 [19.9 kB] Get:51 http://ftpmaster.internal/ubuntu/ trusty/main libjson-c2 armhf 0.11-3ubuntu1 [20.9 kB] Get:52 http://ftpmaster.internal/ubuntu/ trusty/main libkmod2 armhf 15-0ubuntu2 [39.7 kB] Get:53 http://ftpmaster.internal/ubuntu/ trusty/main libnih-dbus1 armhf 1.0.3-4ubuntu24 [15.2 kB] Get:54 http://ftpmaster.internal/ubuntu/ trusty/main libnih1 armhf 1.0.3-4ubuntu24 [50.8 kB] Get:55 http://ftpmaster.internal/ubuntu/ trusty/main udev armhf 204-5ubuntu6 [1019 kB] Get:56 http://ftpmaster.internal/ubuntu/ trusty/main libudev1 armhf 204-5ubuntu6 [37.8 kB] Get:57 http://ftpmaster.internal/ubuntu/ trusty/main libprocps1 armhf 1:3.3.8-2ubuntu1 [32.4 kB] Get:58 http://ftpmaster.internal/ubuntu/ trusty/main procps armhf 1:3.3.8-2ubuntu1 [237 kB] Get:59 http://ftpmaster.internal/ubuntu/ trusty/main initramfs-tools all 0.103ubuntu2 [49.2 kB] Get:60 http://ftpmaster.internal/ubuntu/ trusty/main initramfs-tools-bin armhf 0.103ubuntu2 [9358 B] Get:61 http://ftpmaster.internal/ubuntu/ trusty/main busybox-initramfs armhf 1:1.21.0-1ubuntu1 [169 kB] Get:62 http://ftpmaster.internal/ubuntu/ trusty/main kmod armhf 15-0ubuntu2 [88.0 kB] Get:63 http://ftpmaster.internal/ubuntu/ trusty/main module-init-tools all 15-0ubuntu2 [1874 B] Get:64 http://ftpmaster.internal/ubuntu/ trusty/main plymouth armhf 0.8.8-0ubuntu9 [83.0 kB] Get:65 http://ftpmaster.internal/ubuntu/ trusty/main libpng12-0 armhf 1.2.49-5ubuntu1 [116 kB] Get:66 http://ftpmaster.internal/ubuntu/ trusty/main libplymouth2 armhf 0.8.8-0ubuntu9 [64.3 kB] Get:67 http://ftpmaster.internal/ubuntu/ trusty/main libroken18-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [38.0 kB] Get:68 http://ftpmaster.internal/ubuntu/ trusty/main libasn1-8-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [168 kB] Get:69 http://ftpmaster.internal/ubuntu/ trusty/main libkeyutils1 armhf 1.5.6-1 [6580 B] Get:70 http://ftpmaster.internal/ubuntu/ trusty/main libk5crypto3 armhf 1.11.3+dfsg-3ubuntu2 [94.5 kB] Get:71 http://ftpmaster.internal/ubuntu/ trusty/main libgssapi-krb5-2 armhf 1.11.3+dfsg-3ubuntu2 [108 kB] Get:72 http://ftpmaster.internal/ubuntu/ trusty/main libkrb5-3 armhf 1.11.3+dfsg-3ubuntu2 [292 kB] Get:73 http://ftpmaster.internal/ubuntu/ trusty/main libkrb5support0 armhf 1.11.3+dfsg-3ubuntu2 [28.1 kB] Get:74 http://ftpmaster.internal/ubuntu/ trusty/main libhcrypto4-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [90.0 kB] Get:75 http://ftpmaster.internal/ubuntu/ trusty/main libheimbase1-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [25.8 kB] Get:76 http://ftpmaster.internal/ubuntu/ trusty/main libwind0-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [76.5 kB] Get:77 http://ftpmaster.internal/ubuntu/ trusty/main libhx509-5-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [97.4 kB] Get:78 http://ftpmaster.internal/ubuntu/ trusty/main libkrb5-26-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [180 kB] Get:79 http://ftpmaster.internal/ubuntu/ trusty/main libheimntlm0-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [14.9 kB] Get:80 http://ftpmaster.internal/ubuntu/ trusty/main libgssapi3-heimdal armhf 1.6~git20120403+dfsg1-3ubuntu0.2 [86.2 kB] Get:81 http://ftpmaster.internal/ubuntu/ trusty/main libsasl2-modules-db armhf 2.1.25.dfsg1-17build1 [12.8 kB] Get:82 http://ftpmaster.internal/ubuntu/ trusty/main libsasl2-2 armhf 2.1.25.dfsg1-17build1 [46.0 kB] Get:83 http://ftpmaster.internal/ubuntu/ trusty/main libldap-2.4-2 armhf 2.4.31-1+nmu2ubuntu5 [154 kB] Get:84 http://ftpmaster.internal/ubuntu/ trusty/main libcurl3-gnutls armhf 7.33.0-1ubuntu1 [161 kB] Get:85 http://ftpmaster.internal/ubuntu/ trusty/main libpam-runtime all 1.1.3-10ubuntu1 [40.9 kB] Get:86 http://ftpmaster.internal/ubuntu/ trusty/main adduser all 3.113+nmu3ubuntu3 [169 kB] Get:87 http://ftpmaster.internal/ubuntu/ trusty/main iproute2 armhf 3.12.0-1 [369 kB] Get:88 http://ftpmaster.internal/ubuntu/ trusty/main ifupdown armhf 0.7.46.1ubuntu1 [52.7 kB] Get:89 http://ftpmaster.internal/ubuntu/ trusty/main libjson0 armhf 0.11-3ubuntu1 [1022 B] Get:90 http://ftpmaster.internal/ubuntu/ trusty/main upstart armhf 1.11-0ubuntu1 [628 kB] Get:91 http://ftpmaster.internal/ubuntu/ trusty/main apt-transport-https armhf 0.9.13~exp1ubuntu3 [22.8 kB] Get:92 http://ftpmaster.internal/ubuntu/ trusty/main libsasl2-modules armhf 2.1.25.dfsg1-17build1 [50.6 kB] Get:93 http://ftpmaster.internal/ubuntu/ trusty/main advancecomp armhf 1.18-1 [131 kB] Get:94 http://ftpmaster.internal/ubuntu/ trusty/main dpkg-dev all 1.17.1ubuntu1 [726 kB] Get:95 http://ftpmaster.internal/ubuntu/ trusty/main libdpkg-perl all 1.17.1ubuntu1 [195 kB] Get:96 http://ftpmaster.internal/ubuntu/ trusty/main patch armhf 2.7.1-4 [86.6 kB] Get:97 http://ftpmaster.internal/ubuntu/ trusty-proposed/main build-essential armhf 11.6ubuntu6 [4822 B] Get:98 http://ftpmaster.internal/ubuntu/ trusty/main iproute all 1:3.12.0-1 [2384 B] Get:99 http://ftpmaster.internal/ubuntu/ trusty-proposed/main linux-libc-dev armhf 3.12.0-4.12 [709 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.3 MB in 6s (6755 kB/s) (Reading database ... 11920 files and directories currently installed.) Preparing to replace base-files 6.12ubuntu4 (using .../base-files_6.12ubuntu5_armhf.deb) ... Unpacking replacement base-files ... Setting up base-files (6.12ubuntu5) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11920 files and directories currently installed.) Preparing to replace coreutils 8.20-3ubuntu5 (using .../coreutils_8.21-1ubuntu3_armhf.deb) ... Unpacking replacement coreutils ... Setting up coreutils (8.21-1ubuntu3) ... (Reading database ... 11922 files and directories currently installed.) Preparing to replace diffutils 1:3.2-8 (using .../diffutils_1%3a3.3-1_armhf.deb) ... Unpacking replacement diffutils ... Setting up diffutils (1:3.3-1) ... (Reading database ... 11922 files and directories currently installed.) Preparing to replace dpkg 1.16.12ubuntu1 (using .../dpkg_1.17.1ubuntu1_armhf.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.17.1ubuntu1) ... (Reading database ... 11905 files and directories currently installed.) Preparing to replace findutils 4.4.2-6ubuntu1 (using .../findutils_4.4.2-6ubuntu2_armhf.deb) ... Unpacking replacement findutils ... Setting up findutils (4.4.2-6ubuntu2) ... (Reading database ... 11905 files and directories currently installed.) Preparing to replace grep 2.14-3 (using .../archives/grep_2.15-1_armhf.deb) ... Unpacking replacement grep ... Setting up grep (2.15-1) ... Selecting previously unselected package libdb5.3:armhf. (Reading database ... 11905 files and directories currently installed.) Unpacking libdb5.3:armhf (from .../libdb5.3_5.3.28-3_armhf.deb) ... Setting up libdb5.3:armhf (5.3.28-3) ... Processing triggers for libc-bin ... (Reading database ... 11911 files and directories currently installed.) Preparing to replace perl 5.14.2-21build1 (using .../perl_5.18.1-4build1_armhf.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.14.2-21build1 (using .../perl-base_5.18.1-4build1_armhf.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.18.1-4build1) ... (Reading database ... 11813 files and directories currently installed.) Preparing to replace perl-modules 5.14.2-21build1 (using .../perl-modules_5.18.1-4build1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace bzip2 1.0.6-4 (using .../bzip2_1.0.6-5_armhf.deb) ... Unpacking replacement bzip2 ... Preparing to replace libbz2-1.0:armhf 1.0.6-4 (using .../libbz2-1.0_1.0.6-5_armhf.deb) ... Unpacking replacement libbz2-1.0:armhf ... Setting up libbz2-1.0:armhf (1.0.6-5) ... Processing triggers for libc-bin ... (Reading database ... 11850 files and directories currently installed.) Preparing to replace sed 4.2.2-1ubuntu1 (using .../sed_4.2.2-2ubuntu1_armhf.deb) ... Unpacking replacement sed ... Setting up sed (4.2.2-2ubuntu1) ... (Reading database ... 11850 files and directories currently installed.) Preparing to replace tar 1.26+dfsg-8 (using .../archives/tar_1.27-3_armhf.deb) ... Unpacking replacement tar ... Setting up tar (1.27-3) ... (Reading database ... 11851 files and directories currently installed.) Preparing to replace libgomp1:armhf 4.8.1-10ubuntu8 (using .../libgomp1_4.8.2-5ubuntu3_armhf.deb) ... Unpacking replacement libgomp1:armhf ... Preparing to replace libasan0:armhf 4.8.1-10ubuntu8 (using .../libasan0_4.8.2-5ubuntu3_armhf.deb) ... Unpacking replacement libasan0:armhf ... Preparing to replace gcc-4.8-base:armhf 4.8.1-10ubuntu8 (using .../gcc-4.8-base_4.8.2-5ubuntu3_armhf.deb) ... Unpacking replacement gcc-4.8-base:armhf ... Setting up gcc-4.8-base:armhf (4.8.2-5ubuntu3) ... (Reading database ... 11851 files and directories currently installed.) 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Setting up udev (204-5ubuntu6) ... Installing new version of config file /etc/udev/udev.conf ... Installing new version of config file /etc/init/udevmonitor.conf ... Installing new version of config file /etc/init.d/udev ... invoke-rc.d: policy-rc.d denied execution of restart. Removing 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up initramfs-tools-bin (0.103ubuntu2) ... Setting up busybox-initramfs (1:1.21.0-1ubuntu1) ... Setting up kmod (15-0ubuntu2) ... Setting up module-init-tools (15-0ubuntu2) ... Setting up initramfs-tools (0.103ubuntu2) ... update-initramfs: deferring update (trigger activated) Setting up libpng12-0:armhf (1.2.49-5ubuntu1) ... Setting up libplymouth2:armhf (0.8.8-0ubuntu9) ... Setting up plymouth (0.8.8-0ubuntu9) ... Installing new version of config file /etc/init/plymouth-stop.conf ... update-initramfs: deferring update (trigger activated) Setting up libroken18-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libasn1-8-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libkeyutils1:armhf (1.5.6-1) ... Setting up libkrb5support0:armhf (1.11.3+dfsg-3ubuntu2) ... Setting up libk5crypto3:armhf (1.11.3+dfsg-3ubuntu2) ... Setting up libkrb5-3:armhf (1.11.3+dfsg-3ubuntu2) ... Setting up libgssapi-krb5-2:armhf (1.11.3+dfsg-3ubuntu2) ... Setting up libhcrypto4-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libheimbase1-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libwind0-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libhx509-5-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libkrb5-26-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libheimntlm0-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libgssapi3-heimdal:armhf (1.6~git20120403+dfsg1-3ubuntu0.2) ... Setting up libsasl2-modules-db:armhf (2.1.25.dfsg1-17build1) ... Setting up libsasl2-2:armhf (2.1.25.dfsg1-17build1) ... Setting up libldap-2.4-2:armhf (2.4.31-1+nmu2ubuntu5) ... Setting up libcurl3-gnutls:armhf (7.33.0-1ubuntu1) ... Setting up adduser (3.113+nmu3ubuntu3) ... Setting up iproute2 (3.12.0-1) ... Setting up ifupdown (0.7.46.1ubuntu1) ... Installing new version of config file /etc/init.d/networking ... Setting up libjson0:armhf (0.11-3ubuntu1) ... Setting up upstart (1.11-0ubuntu1) ... Setting up apt-transport-https (0.9.13~exp1ubuntu3) ... Setting up libsasl2-modules:armhf (2.1.25.dfsg1-17build1) ... Setting up advancecomp (1.18-1) ... Setting up patch (2.7.1-4) ... Setting up iproute (1:3.12.0-1) ... Setting up linux-libc-dev:armhf (3.12.0-4.12) ... Setting up perl-modules (5.18.1-4build1) ... Setting up perl (5.18.1-4build1) ... Setting up libdpkg-perl (1.17.1ubuntu1) ... Setting up dpkg-dev (1.17.1ubuntu1) ... Setting up build-essential (11.6ubuntu6) ... Processing triggers for libc-bin ... Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5274657', 'armhf', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '--purpose=PRIMARY', '--architecture=armhf', '--comp=universe', 't-coffee_10.00.r1613-1.dsc'] Initiating build PACKAGEBUILD-5274657 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.2.0-54-highbank #82-Ubuntu SMP PREEMPT Tue Sep 10 20:59:15 UTC 2013 armv7l Automatic build of t-coffee_10.00.r1613-1 on kishi12 by sbuild/armhf 1.170.5 Build started at 20131127-1712 ****************************************************************************** t-coffee_10.00.r1613-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), gfortran Checking for already installed source dependencies... debhelper: missing gfortran: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper gfortran Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libclass-isa-perl libprocps0 libswitch-perl Use 'apt-get autoremove' to remove them. The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libmagic1 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc libgfortran3-dbg groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base gfortran gfortran-4.8 groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libmagic1 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 14.0 MB of archives. After this operation, 47.3 MB of additional disk space will be used. 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Toolchain package versions: libc6-dev_2.17-93ubuntu4 make_3.81-8.2ubuntu3 dpkg-dev_1.17.1ubuntu1 gcc-4.8_4.8.2-5ubuntu3 g++-4.8_4.8.2-5ubuntu3 binutils_2.23.91.20131123-1ubuntu1 libstdc++-4.8-dev_4.8.2-5ubuntu3 libstdc++6_4.8.2-5ubuntu3 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Wed Nov 27 12:50:55 2013 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./t-coffee_10.00.r1613-1.dsc dpkg-source: info: extracting t-coffee in t-coffee-10.00.r1613 dpkg-source: info: unpacking t-coffee_10.00.r1613.orig.tar.gz dpkg-source: info: unpacking t-coffee_10.00.r1613-1.debian.tar.gz dpkg-source: info: applying probconsrna.patch dpkg-buildpackage: source package t-coffee dpkg-buildpackage: source version 10.00.r1613-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build t-coffee-10.00.r1613 dpkg-buildpackage: host architecture armhf /usr/bin/fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source dh_testdir -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/t-coffee-10.00.r1613' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign chmod 644 example/* make[1]: Leaving directory `/build/buildd/t-coffee-10.00.r1613' 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 `/build/buildd/t-coffee-10.00.r1613' dh_auto_build -- -i USER_BIN=../bin/ FCC="gfortran -g -O2" all make[2]: Entering directory `/build/buildd/t-coffee-10.00.r1613/t_coffee_source' 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/Stack.c CC km_coffee/Vector.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/classes.c CC km_coffee/kmeans.c CC dp_lib/util_dp_generic_fasta_nw.c CC dp_lib/util_dp_est.c CC dp_lib/util_dp_gotoh_nw.c CC dp_lib/pavie_dp.c dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': dp_lib/pavie_dp.c:127:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ^ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1079:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ^ dp_lib/pavie_dp.c:1081:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ^ dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': dp_lib/pavie_dp.c:1365:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ^ CC dp_lib/util_dp_clean_maln.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/evaluate_for_domain.c CC dp_lib/util_domain_dp_drivers.c CC dp_lib/fsa_dp.c CC dp_lib/util_dp_drivers.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* align_pdb_pair_2(char*, Constraint_list*)': dp_lib/util_dp_drivers.c:968:35: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)': dp_lib/util_dp_drivers.c:996:35: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1037:33: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c:1048:15: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln1); ^ dp_lib/util_dp_drivers.c:1049:15: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln2); ^ dp_lib/util_dp_drivers.c:1052:17: warning: ignoring return value of 'char* tmpnam(char*)', declared with attribute warn_unused_result [-Wunused-result] tmpnam(hhfile); ^ dp_lib/util_dp_drivers.c:1099:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (buf2, 10000, fp); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1253:31: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1388:33: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1448:33: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1587:33: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* lsqman_pair(char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1662:33: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1734:35: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ dp_lib/util_dp_drivers.c:1785:35: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ^ dp_lib/util_dp_drivers.c:1786:26: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (get_cache_dir()); ^ dp_lib/util_dp_drivers.c:1795:15: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ^ dp_lib/util_dp_drivers.c: In function 'Constraint_list* rna_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1909:31: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^ CC dp_lib/util_dp_mm_nw.c CC dp_lib/evaluate_dirichlet.c dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); ^ dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ^ dp_lib/evaluate_dirichlet.c:323:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ^ dp_lib/evaluate_dirichlet.c:326:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ^ CC dp_lib/util_dp_fasta_nw.c CC dp_lib/util_dp_suboptimal_nw.c CC dp_lib/util_dp_ssec_pwaln.c CC dp_lib/showpair.c CC dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_gotoh_sw.c: In function 'int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_gotoh_sw.c:391:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ^ CC dp_lib/util_dp_fasta_sw.c CC dp_lib/evaluate_for_struc.c CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/util_dp_sim.c CC dp_lib/util_domain_dp.c CC dp_lib/util_graph_maln.c CC dp_lib/evaluate.c dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:774:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &res); ^ dp_lib/evaluate.c:779:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^ dp_lib/evaluate.c:784:38: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:5030:43: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ^ CC t_coffee_lib/t_coffee.c t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:3910:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ^ t_coffee_lib/t_coffee.c:3924:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ^ t_coffee_lib/t_coffee.c:3938:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ^ 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:6814:37: 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:6833:59: 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:6837:41: 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_make_tree.c CC util_lib/util_dps.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:2755:77: 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:2814:32: 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:2819:34: 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:2851:55: 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:2876:27: 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:3841:55: 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/reformat.c util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': 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:10683:35: note: in expansion of macro 'ATOI_ACTION' (D1->A)=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:10688:32: note: in expansion of macro 'ATOI_ACTION' (D1->A)=aln2sample (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:10921:38: 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:11020:38: 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:11021:34: 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:11028:38: 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:11035:35: note: in expansion of macro 'ATOI_ACTION' D1->S=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:11125:44: note: in expansion of macro 'ATOI_ACTION' D1->T= aln2km_tree(D1->A, (ACTION(1)), 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:11230:37: note: in expansion of macro 'ATOI_ACTION' D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^ util_lib/reformat.c:11837:36: 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:11844:10: 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:11845:10: 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:11846:11: 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:11847:11: 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:11848:11: 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:11849:11: 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:11872:34: 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:11996:10: 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:11997:19: 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:12001:27: 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:12520:7: 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:12521:7: 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:12522:8: 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:12523:8: 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:12524:8: 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:1467:34: 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:1505:30: 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:2020:28: 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:3300:26: 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:3307:27: 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:3316:26: 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:3322:36: 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:3324:27: 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:3335:21: 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:3608:46: 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:3611:105: 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:3808:36: 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:3829:63: 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:3834:66: 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:3871:26: 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:3946:27: 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:5114:30: 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:5133:30: 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:5152:25: 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:5505:40: 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:5554:39: 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:5576:39: 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:5774:30: 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:5939:36: 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:12988:41: 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:12998:30: 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:13011:30: 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:13038:22: 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:13149:41: 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.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:242:31: 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:247:31: 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:250:31: 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:267:36: 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:272:34: 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:381:43: 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:808:36: 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:867:38: 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:1223:28: 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:1227:31: 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:1230:33: 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:1231:24: 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:1879:28: 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:5037:34: 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:6496:22: 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:6763:36: 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:6783:30: 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:7119:28: 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:7149:28: 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:7236:43: 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/util_analyse_constraints_list.c CC util_lib/util_aln_analyze.c CC util_lib/util_domain_constraints_list.c CC util_lib/hsearch.c 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:325:29: 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:327:29: 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:333:69: 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:360:29: 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:362:29: 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:370:100: 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/random.c CC util_lib/aln_compare.c CC util_lib/util_declare.c util_lib/util_declare.c: In function 'int read_array_size(void*, size_t)': util_lib/util_declare.c:1568:23: warning: format '%i' expects argument of type 'int', but argument 2 has type 'Memcontrol' [-Wformat=] printf("%i", p[-1]); ^ CC fastal/tree.c CC fastal/fastal_opt_parsing.c CC fastal/fastal.c fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^ fastal/fastal.c:1929:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c:1930:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c:1931:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c:1976:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^ fastal/fastal.c:1980:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c:1981:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c:1982:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2115:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^ fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:2262:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ^ fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': fastal/fastal.c:3323:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^ fastal/fastal.c:3326:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^ fastal/fastal.c:3329:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^ fastal/fastal.c:3331:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^ fastal/fastal.c:3333:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^ fastal/fastal.c:3352:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ^ fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': fastal/fastal.c:3502:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ^ fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': fastal/fastal.c:3575:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/fastal.c:3577:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/fastal.c:3579:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/fastal.c:3581:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/fastal.c:3643:60: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ^ CC fastal/diagonal.c fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': fastal/diagonal.c:434:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ^ fastal/diagonal.c:439:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/diagonal.c:440:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ fastal/diagonal.c:441:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ^ CC fastal/parttree.c fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:26: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ^ fastal/parttree.c:701:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ^ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^ fastal/parttree.c:859:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^ fastal/parttree.c: In function 'int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)': fastal/parttree.c:891:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ fastal/parttree.c:903:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ fastal/parttree.c:906:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ fastal/parttree.c:912:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ fastal/parttree.c: In function 'int euclidean_dist_half(FILE*, long int, short int*, short int*, int)': fastal/parttree.c:951:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ fastal/parttree.c:962:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^ CC fastal/iteration.c fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^ fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': fastal/iteration.c:310:44: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^ fastal/iteration.c:435:17: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command); ^ fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': fastal/iteration.c:501:48: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^ fastal/iteration.c:504:48: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^ fastal/iteration.c:535:49: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ^ fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': fastal/iteration.c:563:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/iteration.c:565:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/iteration.c:567:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ fastal/iteration.c:569:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^ CC fastal/scoring.c fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^ fastal/scoring.c:78:42: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^ fastal/scoring.c:82:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ^ fastal/scoring.c:398:22: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(aln_command); ^ fastal/scoring.c: In function 'void make_ref_alignment(char*, char*, char*, int)': fastal/scoring.c:488:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ^ fastal/scoring.c:502:17: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command); ^ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^ fastal/scoring.c:584:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^ fastal/scoring.c:585:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ^ 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;i= 9 t-coffee is already stripped, ignoring find: `/build/buildd/t-coffee-10.00.r1613/debian/t-coffee-dbgsym': No such file or directory dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dpkg-gencontrol: 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 118 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 pkgstripfiles: Truncating usr/share/doc/t-coffee/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package t-coffee took 0 s dpkg-deb: warning: 'debian/t-coffee/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `t-coffee' in `../t-coffee_10.00.r1613-1_armhf.deb'. dpkg-genchanges -B -mUbuntu/armhf Build Daemon >../t-coffee_10.00.r1613-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build t-coffee-10.00.r1613 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20131127-1717 chroot-autobuild/build/buildd/t-coffee_10.00.r1613-1_armhf.deb: new debian package, version 2.0. size 712760 bytes: control archive= 1268 bytes. 1636 bytes, 30 lines control 333 bytes, 5 lines md5sums Package: t-coffee Version: 10.00.r1613-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1694 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0) Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align Suggests: boxshade, seaview, t-coffee-examples, dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw, amap-align, proda Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. chroot-autobuild/build/buildd/t-coffee_10.00.r1613-1_armhf.deb: drwxr-xr-x root/root 0 2013-11-27 17:17 ./ drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/ drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/bin/ -rwxr-xr-x root/root 1690080 2013-11-27 17:17 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/share/ drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1631 2013-11-25 04:29 ./usr/share/doc/t-coffee/copyright -rw-r--r-- root/root 1363 2013-11-27 17:17 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1744 2008-04-09 13:24 ./usr/share/doc/t-coffee/README.Debian drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/share/man/ drwxr-xr-x root/root 0 2013-11-27 17:17 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2013-11-27 17:17 ./usr/share/man/man1/t_coffee.1.gz t-coffee_10.00.r1613-1_armhf.changes: Format: 1.8 Date: Wed, 27 Nov 2013 21:37:22 +0900 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: armhf Version: 10.00.r1613-1 Distribution: trusty-proposed Urgency: low Maintainer: Ubuntu/armhf Build Daemon Changed-By: Charles Plessy Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Changes: t-coffee (10.00.r1613-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: d5a56aeda19096094c2b5d589e9adf0168ce2f56 712760 t-coffee_10.00.r1613-1_armhf.deb Checksums-Sha256: b122ca58844e206ba01c14a03a6dd7a2cfc7a432d6f9159c84453304f66f24bc 712760 t-coffee_10.00.r1613-1_armhf.deb Files: cebd5b9817c3da881a2cb2f895fefe39 712760 science optional t-coffee_10.00.r1613-1_armhf.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20131127-1717 Build needed 00:05:12, 22404k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5274657'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5274657/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5274657'] Unmounting chroot for build PACKAGEBUILD-5274657... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5274657'] Removing build PACKAGEBUILD-5274657