RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kishi01 3.2.0-98-highbank #138-Ubuntu SMP PREEMPT Mon Jan 11 13:24:41 UTC 2016 armv7l Buildd toolchain package versions: launchpad-buildd_138 python-lpbuildd_138 sbuild_0.65.2-1ubuntu2~ubuntu12.04.1~ppa8 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... 20 May 17:09:22 ntpdate[1078]: adjust time server 10.211.37.1 offset -0.000650 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9779061', '/home/buildd/filecache-default/2569747bf3e651e91ea4c9c8449746fa1ff3dc11'] Unpacking chroot for build PACKAGEBUILD-9779061 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9779061'] Mounting chroot for build PACKAGEBUILD-9779061 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9779061', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-9779061 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9779061', 'armhf'] Updating debian chroot for build PACKAGEBUILD-9779061 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main armhf Packages [1148 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/universe armhf Packages [7489 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4434 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main armhf Packages [64 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe armhf Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main armhf Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe armhf Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf Packages [94.1 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [44.4 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe armhf Packages [246 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [126 kB] Fetched 14.7 MB in 8s (1756 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libpng16-16 The following packages will be upgraded: apt apt-transport-https bash binutils bsdutils bzip2 cpp-5 debconf dmsetup dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasan2 libatomic1 libblkid1 libbz2-1.0 libcap2 libcap2-bin libcc1-0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-5-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libldap-2.4-2 libmount1 libperl5.22 libpng12-0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev lsb-base make mount optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 sed systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata ubuntu-keyring util-linux zlib1g 77 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 80.7 MB of archives. After this operation, 171 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main armhf bash armhf 4.3-14ubuntu2 [502 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf bsdutils armhf 1:2.28-5ubuntu1 [51.6 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main armhf dpkg armhf 1.18.7ubuntu1 [2067 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main armhf grep armhf 2.25-1 [142 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main armhf hostname armhf 3.17ubuntu1 [10.9 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main armhf perl-modules-5.22 all 5.22.2-1 [2642 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main armhf libperl5.22 armhf 5.22.2-1 [2708 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main armhf perl armhf 5.22.2-1 [237 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main armhf perl-base armhf 5.22.2-1 [1183 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main armhf bzip2 armhf 1.0.6-8build1 [31.0 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main armhf libbz2-1.0 armhf 1.0.6-8build1 [29.0 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main armhf zlib1g armhf 1:1.2.8.dfsg-2ubuntu5 [45.4 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf init-system-helpers all 1.33ubuntu2 [31.9 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf init armhf 1.33ubuntu2 [4356 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libsmartcols1 armhf 2.28-5ubuntu1 [56.0 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libuuid1 armhf 2.28-5ubuntu1 [14.4 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libblkid1 armhf 2.28-5ubuntu1 [93.3 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libfdisk1 armhf 2.28-5ubuntu1 [126 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf sysv-rc all 2.88dsf-59.4ubuntu1 [18.2 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf initscripts armhf 2.88dsf-59.4ubuntu1 [23.9 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf util-linux armhf 2.28-5ubuntu1 [821 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf sysvinit-utils armhf 2.88dsf-59.4ubuntu1 [20.3 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main armhf debconf all 1.5.59ubuntu1 [136 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main armhf libgpg-error0 armhf 1.22-2 [29.9 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main armhf libgcrypt20 armhf 1.7.0-2 [335 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main armhf libsystemd0 armhf 229-6ubuntu1 [192 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main armhf systemd armhf 229-6ubuntu1 [3183 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libcap2 armhf 1:2.25-1 [12.3 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main armhf libselinux1 armhf 2.5-3 [56.4 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libmount1 armhf 2.28-5ubuntu1 [103 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libcap2-bin armhf 1:2.25-1 [20.1 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main armhf lsb-base all 9.20160110ubuntu1 [13.7 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf mount armhf 2.28-5ubuntu1 [119 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main armhf sed armhf 4.2.2-7.1 [133 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main armhf tar armhf 1.29-1 [185 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf gcc-6-base armhf 6.1.1-4ubuntu11 [17.2 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libgcc1 armhf 1:6.1.1-4ubuntu11 [38.5 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libstdc++6 armhf 6.1.1-4ubuntu11 [356 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main armhf libapt-pkg5.0 armhf 1.3~exp1 [649 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main armhf ubuntu-keyring all 2016.05.13 [16.5 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main armhf apt armhf 1.3~exp1 [1007 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main armhf systemd-sysv armhf 229-6ubuntu1 [17.7 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main armhf libudev1 armhf 229-6ubuntu1 [54.9 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.124-1ubuntu1 [142 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main armhf libsepol1 armhf 2.5-1 [188 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main armhf libsemanage-common all 2.5-1 [6800 B] Get:47 http://ftpmaster.internal/ubuntu yakkety/main armhf libsemanage1 armhf 2.5-1 [69.3 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main armhf libusb-0.1-4 armhf 2:0.1.12-30 [15.6 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety/main armhf tzdata all 2016d-2 [168 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main armhf libtasn1-6 armhf 4.8-1 [36.9 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libgnutls30 armhf 3.4.11-4ubuntu1 [486 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main armhf libslang2 armhf 2.3.0-2.3ubuntu1 [375 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main armhf apt-transport-https armhf 1.3~exp1 [23.4 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [12.9 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [42.0 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2ubuntu4 [138 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main armhf libpng16-16 armhf 1.6.21-5 [158 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [49.1 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main armhf binutils armhf 2.26-9ubuntu1 [2343 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libgomp1 armhf 6.1.1-4ubuntu11 [67.7 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libatomic1 armhf 6.1.1-4ubuntu11 [6228 B] Get:62 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libasan2 armhf 5.3.1-20ubuntu1 [240 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libubsan0 armhf 6.1.1-4ubuntu11 [95.1 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf g++-5 armhf 5.3.1-20ubuntu1 [25.3 MB] Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libstdc++-5-dev armhf 5.3.1-20ubuntu1 [1433 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf gcc-5 armhf 5.3.1-20ubuntu1 [5540 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libgcc-5-dev armhf 5.3.1-20ubuntu1 [470 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libcc1-0 armhf 6.1.1-4ubuntu11 [26.0 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf cpp-5 armhf 5.3.1-20ubuntu1 [23.7 MB] Get:70 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf gcc-5-base armhf 5.3.1-20ubuntu1 [17.0 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf dmsetup armhf 2:1.02.124-1ubuntu1 [73.3 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main armhf dpkg-dev all 1.18.7ubuntu1 [666 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety/main armhf libdpkg-perl all 1.18.7ubuntu1 [202 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main armhf make armhf 4.1-9 [137 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/universe armhf libpng12-0 armhf 1.2.54-6ubuntu1 [106 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf linux-libc-dev armhf 4.4.0-23.41 [818 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/main armhf optipng armhf 0.7.6-1build1 [79.6 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety/main armhf policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.7 MB in 13s (6195 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 ... 11908 files and directories currently installed.) Preparing to unpack .../bash_4.3-14ubuntu2_armhf.deb ... Unpacking bash (4.3-14ubuntu2) over (4.3-14ubuntu1) ... Setting up bash (4.3-14ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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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 ... 11924 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.0-2_armhf.deb ... Unpacking libgcrypt20:armhf (1.7.0-2) over (1.6.5-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libgcrypt20:armhf (1.7.0-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... 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Setting up ubuntu-keyring (2016.05.13) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: "Ubuntu Archive Automatic Signing Key (2012) " not changed gpg: key EFE21092: "Ubuntu CD Image Automatic Signing Key (2012) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 (Reading database ... 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(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 ... 11927 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.5-1_armhf.deb ... Unpacking libsemanage1:armhf (2.5-1) over (2.3-1build3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libsemanage1:armhf (2.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libusb-0.1-4_2%3a0.1.12-30_armhf.deb ... Unpacking libusb-0.1-4:armhf (2:0.1.12-30) over (2:0.1.12-28) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libusb-0.1-4:armhf (2:0.1.12-30) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... 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Setting up sysv-rc (2.88dsf-59.4ubuntu1) ... Setting up initscripts (2.88dsf-59.4ubuntu1) ... Installing new version of config file /etc/init.d/ondemand ... Installing new version of config file /etc/init.d/sendsigs ... Installing new version of config file /etc/init.d/umountroot ... Setting up tzdata (2016d-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 20 17:12:02 UTC 2016. Universal Time is now: Fri May 20 17:12:02 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtasn1-6:armhf (4.8-1) ... Setting up libgnutls30:armhf (3.4.11-4ubuntu1) ... Setting up libslang2:armhf (2.3.0-2.3ubuntu1) ... Setting up apt-transport-https (1.3~exp1) ... Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-15) ... Setting up libsasl2-2:armhf (2.1.26.dfsg1-15) ... Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2ubuntu4) ... Setting up libpng16-16:armhf (1.6.21-5) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ... Setting up binutils (2.26-9ubuntu1) ... Setting up libgomp1:armhf (6.1.1-4ubuntu11) ... Setting up libatomic1:armhf (6.1.1-4ubuntu11) ... Setting up gcc-5-base:armhf (5.3.1-20ubuntu1) ... Setting up libasan2:armhf (5.3.1-20ubuntu1) ... Setting up libubsan0:armhf (6.1.1-4ubuntu11) ... Setting up cpp-5 (5.3.1-20ubuntu1) ... Setting up libcc1-0:armhf (6.1.1-4ubuntu11) ... Setting up libgcc-5-dev:armhf (5.3.1-20ubuntu1) ... Setting up gcc-5 (5.3.1-20ubuntu1) ... Setting up libstdc++-5-dev:armhf (5.3.1-20ubuntu1) ... Setting up g++-5 (5.3.1-20ubuntu1) ... Setting up dmsetup (2:1.02.124-1ubuntu1) ... Setting up libdpkg-perl (1.18.7ubuntu1) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.7ubuntu1) ... Setting up libpng12-0:armhf (1.2.54-6ubuntu1) ... Setting up linux-libc-dev:armhf (4.4.0-23.41) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9779061', 'armhf', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'wise_2.4.1-18.dsc'] Initiating build PACKAGEBUILD-9779061 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.2.0-98-highbank #138-Ubuntu SMP PREEMPT Mon Jan 11 13:24:41 UTC 2016 armv7l sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on kishi01.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ wise 2.4.1-18 (armhf) 20 May 2016 17:12 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: wise Version: 2.4.1-18 Source Version: 2.4.1-18 Distribution: yakkety-proposed Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/wise-E4Lw0H/wise-2.4.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/wise-E4Lw0H' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9779061/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── wise_2.4.1-18.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-34JB2l/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ Packages [524 B] Fetched 2851 B in 0s (100 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-34JB2l/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 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 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 copy:/«BUILDDIR»/resolver-34JB2l/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) 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 ... 11969 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev 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), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev dpkg-deb: building package 'sbuild-build-depends-wise-dummy' in '/«BUILDDIR»/resolver-Vvxgx5/apt_archive/sbuild-build-depends-wise-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ Sources [460 B] Get:5 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ Packages [728 B] Fetched 3307 B in 0s (117 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install wise build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpoppler58 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsm6 libsp1c2 libsynctex1 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtool libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal sgml-base sgml-data sp t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base ucf x11-common xdg-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make docbook-defguide docbook-dsssl docbook-xml psgml gettext-doc ghostscript-x hpijs groff hevea-doc texlive-latex-extra cups-common libglib2.0-doc fonts-droid texlive-lang-cjk liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc binfmt-support sgml-base-doc perlsgml w3-recs opensp libxml2-utils doc-base perl-tk xpdf-reader | pdf-viewer dvidvi latexdiff lacheck xindy fragmaster latexmk dvipng chktex purifyeps gvfs-bin Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev dbus shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl lmodern ruby wish libyaml-tiny-perl ruby | ruby-interpreter texlive-latex-recommended libfile-homedir-perl texlive-latex-base-doc libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpoppler58 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsm6 libsp1c2 libsynctex1 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtool libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal sbuild-build-depends-wise-dummy sgml-base sgml-data sp t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base ucf x11-common xdg-utils xml-core zlib1g-dev 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 74.2 MB of archives. After this operation, 261 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-wise-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-Vvxgx5/apt_archive ./ sbuild-build-depends-wise-dummy 0.invalid.0 [966 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main armhf libxau6 armhf 1:1.0.8-1 [7324 B] Get:3 http://ftpmaster.internal/ubuntu yakkety/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [9620 B] Get:4 http://ftpmaster.internal/ubuntu yakkety/main armhf libxcb1 armhf 1.11.1-1ubuntu1 [36.4 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main armhf libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main armhf libx11-6 armhf 2:1.6.3-1ubuntu2 [514 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main armhf libxext6 armhf 2:1.3.3-1 [25.1 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main armhf groff-base armhf 1.22.3-7 [1023 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main armhf bsdmainutils armhf 9.0.6ubuntu3 [169 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main armhf libpipeline1 armhf 1.4.1-2 [21.0 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main armhf man-db armhf 2.7.5-1 [836 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main armhf sgml-base all 1.26+nmu4ubuntu1 [12.5 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main armhf x11-common all 1:7.7+13ubuntu3 [22.4 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main armhf libice6 armhf 2:1.0.9-1 [32.7 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main armhf libjpeg-turbo8 armhf 1.4.2-0ubuntu3 [87.3 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main armhf libpcrecpp0v5 armhf 2:8.38-3.1 [13.2 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main armhf libsm6 armhf 2:1.2.2-1 [13.9 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main armhf libunistring0 armhf 0.9.3-5.2ubuntu1 [250 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main armhf libxpm4 armhf 1:3.5.11-1 [28.6 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main armhf libzzip-0-13 armhf 0.13.62-3 [22.2 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main armhf poppler-data all 0.4.7-7 [1495 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main armhf libpython2.7-minimal armhf 2.7.11-9 [335 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main armhf python2.7-minimal armhf 2.7.11-9 [1114 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main armhf python-minimal armhf 2.7.11-1 [28.2 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main armhf mime-support all 3.59ubuntu1 [31.0 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf libexpat1 armhf 2.1.1-1ubuntu1 [52.8 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main armhf libpython2.7-stdlib armhf 2.7.11-9 [1817 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main armhf python2.7 armhf 2.7.11-9 [221 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main armhf libpython-stdlib armhf 2.7.11-1 [7640 B] Get:30 http://ftpmaster.internal/ubuntu yakkety/main armhf python armhf 2.7.11-1 [137 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main armhf libjbig0 armhf 2.1-3.1 [24.3 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main armhf libmagic1 armhf 1:5.25-2ubuntu1 [211 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main armhf file armhf 1:5.25-2ubuntu1 [20.9 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main armhf ucf all 3.0036 [52.9 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main armhf libasprintf0v5 armhf 0.19.7-2ubuntu3 [6158 B] Get:36 http://ftpmaster.internal/ubuntu yakkety/main armhf gettext-base armhf 0.19.7-2ubuntu3 [44.5 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main armhf libdbus-1-3 armhf 1.10.6-1ubuntu3 [141 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main armhf libelf1 armhf 0.165-3ubuntu1 [40.2 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main armhf libglib2.0-0 armhf 2.48.1-1 [977 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main armhf libglib2.0-data all 2.48.1-1 [131 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main armhf libicu57 armhf 57.1-1 [7424 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main armhf libxml2 armhf 2.9.3+dfsg1-1build1 [601 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main armhf xml-core all 0.13+nmu2 [23.3 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main armhf libsigsegv2 armhf 2.10-5 [13.3 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main armhf m4 armhf 1.4.17-5 [179 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf autoconf all 2.69-10 [321 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety-proposed/main armhf autotools-dev all 20160430.1 [39.6 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main armhf automake all 1:1.15-4ubuntu1 [510 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety/main armhf autopoint all 0.19.7-2ubuntu3 [406 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main armhf libcroco3 armhf 0.6.11-1 [70.0 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main armhf gettext armhf 0.19.7-2ubuntu3 [1013 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main armhf po-debconf all 1.0.19 [234 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main armhf libarchive-zip-perl all 1.57-1 [84.0 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main armhf dh-strip-nondeterminism all 0.016-1 [4858 B] Get:58 http://ftpmaster.internal/ubuntu yakkety/main armhf libtool all 2.4.6-0.1 [193 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main armhf dh-autoreconf all 12 [15.8 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety/main armhf debhelper all 9.20160403ubuntu1 [711 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety/main armhf sgml-data all 2.0.10 [173 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/universe armhf docbook all 4.5-6 [122 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/universe armhf libsp1c2 armhf 1.3.4-1.2.1-49ubuntu1 [907 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety/universe armhf sp armhf 1.3.4-1.2.1-49ubuntu1 [115 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety/universe armhf docbook-to-man armhf 1:2.0.0-34 [68.9 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main armhf fonts-dejavu-core all 2.35-1 [1039 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main armhf fontconfig-config all 2.11.94-0ubuntu1 [49.9 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main armhf libavahi-common-data armhf 0.6.32~rc+dfsg-1ubuntu2 [21.9 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety/main armhf libavahi-common3 armhf 0.6.32~rc+dfsg-1ubuntu2 [18.5 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main armhf libavahi-client3 armhf 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety/main armhf libcups2 armhf 2.1.3-5 [169 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:73 http://ftpmaster.internal/ubuntu yakkety/main armhf libtiff5 armhf 4.0.6-1 [128 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main armhf libcupsfilters1 armhf 1.8.3-2ubuntu4 [73.4 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main armhf libcupsimage2 armhf 2.1.3-5 [14.3 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety/main armhf libfreetype6 armhf 2.6.3-3ubuntu1 [272 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/main armhf libfontconfig1 armhf 2.11.94-0ubuntu1 [114 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety/main armhf libijs-0.35 armhf 0.35-12 [14.0 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety/main armhf libjbig2dec0 armhf 0.13-2 [47.8 kB] Get:80 http://ftpmaster.internal/ubuntu yakkety/main armhf liblcms2-2 armhf 2.7-1ubuntu1 [114 kB] Get:81 http://ftpmaster.internal/ubuntu yakkety/main armhf libpaper1 armhf 1.1.24+nmu4ubuntu1 [13.0 kB] Get:82 http://ftpmaster.internal/ubuntu yakkety/main armhf libgs9-common all 9.18~dfsg~0-0ubuntu5 [2982 kB] Get:83 http://ftpmaster.internal/ubuntu yakkety/main armhf libgs9 armhf 9.18~dfsg~0-0ubuntu5 [1774 kB] Get:84 http://ftpmaster.internal/ubuntu yakkety/main armhf gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1 [3374 kB] Get:85 http://ftpmaster.internal/ubuntu yakkety/main armhf ghostscript armhf 9.18~dfsg~0-0ubuntu5 [40.7 kB] Get:86 http://ftpmaster.internal/ubuntu yakkety/main armhf libnetpbm10 armhf 2:10.0-15.3build1 [47.5 kB] Get:87 http://ftpmaster.internal/ubuntu yakkety/main armhf netpbm armhf 2:10.0-15.3build1 [891 kB] Get:88 http://ftpmaster.internal/ubuntu yakkety/main armhf tex-common all 6.05 [545 kB] Get:89 http://ftpmaster.internal/ubuntu yakkety/main armhf xdg-utils all 1.1.1-1ubuntu1 [59.9 kB] Get:90 http://ftpmaster.internal/ubuntu yakkety/main armhf libpaper-utils armhf 1.1.24+nmu4ubuntu1 [8000 B] Get:91 http://ftpmaster.internal/ubuntu yakkety/main armhf libkpathsea6 armhf 2016.20160513.41080-2 [47.3 kB] Get:92 http://ftpmaster.internal/ubuntu yakkety/main armhf libptexenc1 armhf 2016.20160513.41080-2 [32.3 kB] Get:93 http://ftpmaster.internal/ubuntu yakkety/main armhf libsynctex1 armhf 2016.20160513.41080-2 [35.7 kB] Get:94 http://ftpmaster.internal/ubuntu yakkety/main armhf libtexlua52 armhf 2016.20160513.41080-2 [69.1 kB] Get:95 http://ftpmaster.internal/ubuntu yakkety/main armhf libtexluajit2 armhf 2016.20160513.41080-2 [180 kB] Get:96 http://ftpmaster.internal/ubuntu yakkety/main armhf t1utils armhf 1.39-2 [47.2 kB] Get:97 http://ftpmaster.internal/ubuntu yakkety/main armhf libpixman-1-0 armhf 0.33.6-1 [158 kB] Get:98 http://ftpmaster.internal/ubuntu yakkety/main armhf libxcb-render0 armhf 1.11.1-1ubuntu1 [10.9 kB] Get:99 http://ftpmaster.internal/ubuntu yakkety/main armhf libxcb-shm0 armhf 1.11.1-1ubuntu1 [5398 B] Get:100 http://ftpmaster.internal/ubuntu yakkety/main armhf libxrender1 armhf 1:0.9.9-0ubuntu1 [15.7 kB] Get:101 http://ftpmaster.internal/ubuntu yakkety/main armhf libcairo2 armhf 1.14.6-1build1 [489 kB] Get:102 http://ftpmaster.internal/ubuntu yakkety/main armhf libgraphite2-3 armhf 1.3.6-1ubuntu1 [56.5 kB] Get:103 http://ftpmaster.internal/ubuntu yakkety/main armhf libharfbuzz0b armhf 1.2.6-2 [158 kB] Get:104 http://ftpmaster.internal/ubuntu yakkety/main armhf libharfbuzz-icu0 armhf 1.2.6-2 [4852 B] Get:105 http://ftpmaster.internal/ubuntu yakkety/main armhf libpoppler58 armhf 0.41.0-0ubuntu2 [649 kB] Get:106 http://ftpmaster.internal/ubuntu yakkety/main armhf libpotrace0 armhf 1.13-2 [15.1 kB] Get:107 http://ftpmaster.internal/ubuntu yakkety/main armhf libxt6 armhf 1:1.1.5-0ubuntu1 [130 kB] Get:108 http://ftpmaster.internal/ubuntu yakkety/main armhf libxmu6 armhf 2:1.1.2-2 [38.3 kB] Get:109 http://ftpmaster.internal/ubuntu yakkety/main armhf libxaw7 armhf 2:1.0.13-1 [141 kB] Get:110 http://ftpmaster.internal/ubuntu yakkety/main armhf libxi6 armhf 2:1.7.6-1 [24.5 kB] Get:111 http://ftpmaster.internal/ubuntu yakkety/main armhf texlive-binaries armhf 2016.20160513.41080-2 [4616 kB] Get:112 http://ftpmaster.internal/ubuntu yakkety/main armhf texlive-base all 2016.20160512-1 [15.7 MB] Get:113 http://ftpmaster.internal/ubuntu yakkety/universe armhf ocaml-base-nox armhf 4.02.3-6ubuntu2 [431 kB] Get:114 http://ftpmaster.internal/ubuntu yakkety/universe armhf hevea all 2.28-1 [880 kB] Get:115 http://ftpmaster.internal/ubuntu yakkety/main armhf libglib2.0-bin armhf 2.48.1-1 [37.6 kB] Get:116 http://ftpmaster.internal/ubuntu yakkety/main armhf libpcre16-3 armhf 2:8.38-3.1 [125 kB] Get:117 http://ftpmaster.internal/ubuntu yakkety/main armhf libpcre32-3 armhf 2:8.38-3.1 [119 kB] Get:118 http://ftpmaster.internal/ubuntu yakkety/main armhf libpcre3-dev armhf 2:8.38-3.1 [464 kB] Get:119 http://ftpmaster.internal/ubuntu yakkety/main armhf pkg-config armhf 0.29.1-0ubuntu1 [42.2 kB] Get:120 http://ftpmaster.internal/ubuntu yakkety/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2ubuntu5 [161 kB] Get:121 http://ftpmaster.internal/ubuntu yakkety/main armhf libglib2.0-dev armhf 2.48.1-1 [1281 kB] Get:122 http://ftpmaster.internal/ubuntu yakkety/main armhf texlive-latex-base all 2016.20160512-1 [842 kB] Get:123 http://ftpmaster.internal/ubuntu yakkety/main armhf texlive-extra-utils all 2016.20160512-1 [11.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.2 MB in 5s (12.9 MB/s) Selecting previously unselected package libxau6:armhf. (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 ... 11969 files and directories currently installed.) Preparing to unpack .../libxau6_1%3a1.0.8-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-1.1) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_armhf.deb ... 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(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 ... 14152 files and directories currently installed.) Preparing to unpack .../python_2.7.11-1_armhf.deb ... Unpacking python (2.7.11-1) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../libjbig0_2.1-3.1_armhf.deb ... Unpacking libjbig0:armhf (2.1-3.1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_armhf.deb ... Unpacking libmagic1:armhf (1:5.25-2ubuntu1) ... 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Setting up libx11-6:armhf (2:1.6.3-1ubuntu2) ... Setting up libxext6:armhf (2:1.3.3-1) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... 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 (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sgml-base (1.26+nmu4ubuntu1) ... Setting up x11-common (1:7.7+13ubuntu3) ... 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 libice6:armhf (2:1.0.9-1) ... Setting up libjpeg-turbo8:armhf (1.4.2-0ubuntu3) ... Setting up libpcrecpp0v5:armhf (2:8.38-3.1) ... Setting up libsm6:armhf (2:1.2.2-1) ... Setting up libunistring0:armhf (0.9.3-5.2ubuntu1) ... Setting up libxpm4:armhf (1:3.5.11-1) ... Setting up libzzip-0-13:armhf (0.13.62-3) ... Setting up poppler-data (0.4.7-7) ... Setting up mime-support (3.59ubuntu1) ... Setting up libexpat1:armhf (2.1.1-1ubuntu1) ... Setting up libpython2.7-stdlib:armhf (2.7.11-9) ... Setting up python2.7 (2.7.11-9) ... Setting up libpython-stdlib:armhf (2.7.11-1) ... Setting up python (2.7.11-1) ... Setting up libjbig0:armhf (2.1-3.1) ... Setting up libmagic1:armhf (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up ucf (3.0036) ... Setting up libasprintf0v5:armhf (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libdbus-1-3:armhf (1.10.6-1ubuntu3) ... Setting up libelf1:armhf (0.165-3ubuntu1) ... Setting up libglib2.0-0:armhf (2.48.1-1) ... No schema files found: doing nothing. Setting up libglib2.0-data (2.48.1-1) ... Setting up libicu57:armhf (57.1-1) ... Setting up libxml2:armhf (2.9.3+dfsg1-1build1) ... Setting up xml-core (0.13+nmu2) ... Setting up libsigsegv2:armhf (2.10-5) ... Setting up m4 (1.4.17-5) ... Setting up autoconf (2.69-10) ... Setting up autotools-dev (20160430.1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.7-2ubuntu3) ... Setting up libcroco3:armhf (0.6.11-1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.57-1) ... Setting up libfile-stripnondeterminism-perl (0.016-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.6-0.1) ... Setting up libsp1c2 (1.3.4-1.2.1-49ubuntu1) ... Setting up sp (1.3.4-1.2.1-49ubuntu1) ... Setting up fonts-dejavu-core (2.35-1) ... Setting up fontconfig-config (2.11.94-0ubuntu1) ... Setting up libavahi-common-data:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-common3:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-client3:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libcups2:armhf (2.1.3-5) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libtiff5:armhf (4.0.6-1) ... Setting up libcupsfilters1:armhf (1.8.3-2ubuntu4) ... Setting up libcupsimage2:armhf (2.1.3-5) ... Setting up libfreetype6:armhf (2.6.3-3ubuntu1) ... Setting up libfontconfig1:armhf (2.11.94-0ubuntu1) ... Setting up libijs-0.35:armhf (0.35-12) ... Setting up libjbig2dec0:armhf (0.13-2) ... Setting up liblcms2-2:armhf (2.7-1ubuntu1) ... Setting up libpaper1:armhf (1.1.24+nmu4ubuntu1) ... Creating config file /etc/papersize with new version Setting up libgs9-common (9.18~dfsg~0-0ubuntu5) ... update-alternatives: using /usr/share/ghostscript/9.18 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9:armhf (9.18~dfsg~0-0ubuntu5) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Setting up ghostscript (9.18~dfsg~0-0ubuntu5) ... Setting up libnetpbm10 (2:10.0-15.3build1) ... Setting up netpbm (2:10.0-15.3build1) ... Setting up tex-common (6.05) ... update-language: texlive-base not installed and configured, doing nothing! Setting up xdg-utils (1.1.1-1ubuntu1) ... Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ... Setting up libkpathsea6:armhf (2016.20160513.41080-2) ... Setting up libptexenc1:armhf (2016.20160513.41080-2) ... Setting up libsynctex1:armhf (2016.20160513.41080-2) ... Setting up libtexlua52:armhf (2016.20160513.41080-2) ... Setting up libtexluajit2:armhf (2016.20160513.41080-2) ... Setting up t1utils (1.39-2) ... Setting up libpixman-1-0:armhf (0.33.6-1) ... Setting up libxcb-render0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-shm0:armhf (1.11.1-1ubuntu1) ... Setting up libxrender1:armhf (1:0.9.9-0ubuntu1) ... Setting up libcairo2:armhf (1.14.6-1build1) ... Setting up libgraphite2-3:armhf (1.3.6-1ubuntu1) ... Setting up libharfbuzz0b:armhf (1.2.6-2) ... Setting up libharfbuzz-icu0:armhf (1.2.6-2) ... Setting up libpoppler58:armhf (0.41.0-0ubuntu2) ... Setting up libpotrace0 (1.13-2) ... Setting up libxt6:armhf (1:1.1.5-0ubuntu1) ... Setting up libxmu6:armhf (2:1.1.2-2) ... Setting up libxaw7:armhf (2:1.0.13-1) ... Setting up libxi6:armhf (2:1.7.6-1) ... Setting up texlive-binaries (2016.20160513.41080-2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up ocaml-base-nox (4.02.3-6ubuntu2) ... Setting up libglib2.0-bin (2.48.1-1) ... Setting up libpcre16-3:armhf (2:8.38-3.1) ... Setting up libpcre32-3:armhf (2:8.38-3.1) ... Setting up libpcre3-dev:armhf (2:8.38-3.1) ... Setting up pkg-config (0.29.1-0ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2ubuntu5) ... Setting up libglib2.0-dev (2.48.1-1) ... Processing triggers for tex-common (6.05) ... update-language: texlive-base not installed and configured, doing nothing! texlive-base is not ready, skipping fmtutil --all call Setting up texlive-base (2016.20160512-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up sgml-data (2.0.10) ... Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up hevea (2.28-1) ... Setting up texlive-latex-base (2016.20160512-1) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up docbook (4.5-6) ... Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-extra-utils (2016.20160512-1) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up docbook-to-man (1:2.0.0-34) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for tex-common (6.05) ... Building format(s) --all. This may take some time... done. Setting up sbuild-build-depends-wise-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-98-highbank armhf (armv7l) Toolchain package versions: binutils_2.26-9ubuntu1 dpkg-dev_1.18.7ubuntu1 g++-5_5.3.1-20ubuntu1 gcc-5_5.3.1-20ubuntu1 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-20ubuntu1 libstdc++6_6.1.1-4ubuntu11 linux-libc-dev_4.4.0-23.41 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3~exp1 apt-transport-https_1.3~exp1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28-5ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-20ubuntu1 dash_0.5.8-2.1ubuntu2 debconf_1.5.59ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1ubuntu1 docbook_4.5-6 docbook-to-man_1:2.0.0-34 dpkg_1.18.7ubuntu1 dpkg-dev_1.18.7ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 fontconfig-config_2.11.94-0ubuntu1 fonts-dejavu-core_2.35-1 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-20ubuntu1 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-20ubuntu1 gcc-5-base_5.3.1-20ubuntu1 gcc-6-base_6.1.1-4ubuntu11 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 ghostscript_9.18~dfsg~0-0ubuntu5 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1 gzip_1.6-4ubuntu1 hevea_2.28-1 hostname_3.17ubuntu1 init_1.33ubuntu2 init-system-helpers_1.33ubuntu2 initscripts_2.88dsf-59.4ubuntu1 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.3~exp1 libarchive-zip-perl_1.57-1 libasan2_5.3.1-20ubuntu1 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_6.1.1-4ubuntu11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libavahi-client3_0.6.32~rc+dfsg-1ubuntu2 libavahi-common-data_0.6.32~rc+dfsg-1ubuntu2 libavahi-common3_0.6.32~rc+dfsg-1ubuntu2 libblkid1_2.28-5ubuntu1 libbz2-1.0_1.0.6-8build1 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcairo2_1.14.6-1build1 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-4ubuntu11 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcups2_2.1.3-5 libcupsfilters1_1.8.3-2ubuntu4 libcupsimage2_2.1.3-5 libcurl3-gnutls_7.47.0-1ubuntu2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu3 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.124-1ubuntu1 libdpkg-perl_1.18.7ubuntu1 libelf1_0.165-3ubuntu1 libexpat1_2.1.1-1ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.28-5ubuntu1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libfontconfig1_2.11.94-0ubuntu1 libfreetype6_2.6.3-3ubuntu1 libgcc-5-dev_5.3.1-20ubuntu1 libgcc1_1:6.1.1-4ubuntu11 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libglib2.0-bin_2.48.1-1 libglib2.0-data_2.48.1-1 libglib2.0-dev_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.11-4ubuntu1 libgomp1_6.1.1-4ubuntu11 libgpg-error0_1.22-2 libgraphite2-3_1.3.6-1ubuntu1 libgs9_9.18~dfsg~0-0ubuntu5 libgs9-common_9.18~dfsg~0-0ubuntu5 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libharfbuzz-icu0_1.2.6-2 libharfbuzz0b_1.2.6-2 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.2-1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libice6_2:1.0.9-1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libijs-0.35_0.35-12 libisl15_0.16.1-1 libjbig0_2.1-3.1 libjbig2dec0_0.13-2 libjpeg-turbo8_1.4.2-0ubuntu3 libjpeg8_8c-2ubuntu8 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkpathsea6_2016.20160513.41080-2 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblcms2-2_2.7-1ubuntu1 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.28-5ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnetpbm10_2:10.0-15.3build1 libnettle6_3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpaper-utils_1.1.24+nmu4ubuntu1 libpaper1_1.1.24+nmu4ubuntu1 libpcre16-3_2:8.38-3.1 libpcre3_2:8.38-3.1 libpcre3-dev_2:8.38-3.1 libpcre32-3_2:8.38-3.1 libpcrecpp0v5_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-5 libpoppler58_0.41.0-0ubuntu2 libpotrace0_1.13-2 libprocps4_2:3.3.10-4ubuntu2 libptexenc1_2016.20160513.41080-2 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-9 libpython2.7-stdlib_2.7.11-9 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.28-5ubuntu1 libsp1c2_1.3.4-1.2.1-49ubuntu1 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-20ubuntu1 libstdc++6_6.1.1-4ubuntu11 libsynctex1_2016.20160513.41080-2 libsystemd0_229-6ubuntu1 libtasn1-6_4.8-1 libtexlua52_2016.20160513.41080-2 libtexluajit2_2016.20160513.41080-2 libtiff5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtool_2.4.6-0.1 libubsan0_6.1.1-4ubuntu11 libudev1_229-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5ubuntu1 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1ubuntu1 libxcb-shm0_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxi6_2:1.7.6-1 libxml2_2.9.3+dfsg1-1build1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1 libxrender1_1:0.9.9-0ubuntu1 libxt6_1:1.1.5-0ubuntu1 libzzip-0-13_0.13.62-3 linux-libc-dev_4.4.0-23.41 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110ubuntu1 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.28-5ubuntu1 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 netpbm_2:10.0-15.3build1 ocaml-base-nox_4.02.3-6ubuntu2 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-config_0.29.1-0ubuntu1 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 poppler-data_0.4.7-7 procps_2:3.3.10-4ubuntu2 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-9 python2.7-minimal_2.7.11-9 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-wise-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4ubuntu1 sgml-data_2.0.10 sp_1.3.4-1.2.1-49ubuntu1 systemd_229-6ubuntu1 systemd-sysv_229-6ubuntu1 sysv-rc_2.88dsf-59.4ubuntu1 sysvinit-utils_2.88dsf-59.4ubuntu1 t1utils_1.39-2 tar_1.29-1 tex-common_6.05 texlive-base_2016.20160512-1 texlive-binaries_2016.20160513.41080-2 texlive-extra-utils_2016.20160512-1 texlive-latex-base_2016.20160512-1 tzdata_2016d-2 ubuntu-keyring_2016.05.13 ucf_3.0036 util-linux_2.28-5ubuntu1 x11-common_1:7.7+13ubuntu3 xdg-utils_1.1.1-1ubuntu1 xml-core_0.13+nmu2 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Thu May 19 23:08:27 2016 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./wise_2.4.1-18.dsc dpkg-source: info: extracting wise in wise-2.4.1 dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-18.debian.tar.xz dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-source: info: applying 11_consistent_manual_dates.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 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: info: source package wise dpkg-buildpackage: info: source version 2.4.1-18 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build wise-2.4.1 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/«PKGBUILDDIR»' /usr/bin/make -C src clean make[2]: Entering directory '/«PKGBUILDDIR»/src' cd external ; /usr/bin/make clean make[3]: Entering directory '/«PKGBUILDDIR»/src/external' (cd mott; make clean) make[4]: Entering directory '/«PKGBUILDDIR»/src/external/mott' rm -f *.[oa] make[4]: Leaving directory '/«PKGBUILDDIR»/src/external/mott' make[3]: Leaving directory '/«PKGBUILDDIR»/src/external' if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi if test -d socket; then cd socket ; rm -f *.[oa]; fi if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi if test -d network; then cd network ; rm -f *.[oa]; fi if test -d dyc; then cd dyc ; rm -f *.[oa]; fi if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi make[2]: Leaving directory '/«PKGBUILDDIR»/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory '/«PKGBUILDDIR»/debian/manpages.d' rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 make[2]: Leaving directory '/«PKGBUILDDIR»/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server rm -f docs/temp.tex rm -f docs/api.* rm -f docs/wise2.image.tex rm -f docs/*.pdf rm -f docs/*.aux rm -f docs/*.log rm -f docs/*.toc rm -f docs/*.pdf rm -f docs/*.dvi rm -f docs/*.ps rm -f docs/*.4ct rm -f docs/*.4tc rm -f docs/*.css rm -f docs/*.idv rm -f docs/*.lg rm -f docs/*.tmp rm -f docs/*.xref rm -f docs/*.haux rm -f docs/*.htoc rm -f docs/*.html rm -f -r docs/api rm -f -r docs/dynamite rm -f -r docs/wise2 dh_clean rm -f debian/debhelper-build-stamp rm -f debian/wise.substvars rm -f debian/wise.*.debhelper rm -rf debian/wise/ rm -f debian/wise-doc.substvars rm -f debian/wise-doc.*.debhelper rm -rf debian/wise-doc/ rm -f debian/wise-data.substvars rm -f debian/wise-data.*.debhelper rm -rf debian/wise-data/ rm -rf debian/.debhelper/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/«PKGBUILDDIR»' /usr/bin/make -C src all make[2]: Entering directory '/«PKGBUILDDIR»/src' (cd base ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/«PKGBUILDDIR»/src/base' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseconfig.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisestring.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseerror.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisememman.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisefile.c wisefile.dy: In function ‘Wise2_myfclose’: wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE * {aka struct _IO_FILE *}’ [-Wformat=] fprintf(stderr,"Closing %d\n",ofp); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiserandom.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisetime.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseoverlay.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisestreaminterface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include commandline.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[3]: Leaving directory '/«PKGBUILDDIR»/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/«PKGBUILDDIR»/src/HMMer2' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c alphabet.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c core_algorithms.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c debug.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c emit.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c emulation.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c histogram.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c hmmio.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c mathsupport.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c masks.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c misc.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c modelmakers.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c plan7.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c plan9.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c prior.c prior.c: In function ‘P7ReadPrior’: prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c tophits.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c trace.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c aligneval.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c alignio.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c cluster.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c dayhoff.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c file.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c getopt.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c gnuregex.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c interleaved.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c iupac.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c msf.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c revcomp.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c selex.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sqerror.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sqio.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_ctype.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_math.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_string.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c stack.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c translate.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c types.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[3]: Leaving directory '/«PKGBUILDDIR»/src/HMMer2' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/«PKGBUILDDIR»/src/dynlibsrc' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ packaln.c packaln.dy: In function ‘Wise2_read_simple_PackAln’: packaln.dy:88:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,ifp); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ aln.c aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dnamatrix.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ probability.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ alnrange.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ alnconvert.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ basematrix.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shattermatrix.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ matrixdebug.c matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’: matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,in); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dpenvelope.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dbsearchimpl.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dprunimpl.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexsequence.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexevalset.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexconsensi.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequence.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequencestream.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ seqalign.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hitlist.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsp.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspstream.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codon.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ compmat.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codonmatrix.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codonmapper.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequencedb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hscore.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ seqlookup.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ arrayseqlookup.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genericindexresult.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ singlenumberspace.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ histogram.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ searchstatinterface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ searchstatlookup.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteindb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ protein.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ pairbase.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ pairbaseseq.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomicdb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ randommodel.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ randomdb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomic.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ cdna.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ cdnadb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dna.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ embl.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomicregion.c genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’: genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,maxlen,ifp); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ gene.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ transcript.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ translation.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ btcanvas.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ asciibtcanvas.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[3]: Leaving directory '/«PKGBUILDDIR»/src/dynlibsrc' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/«PKGBUILDDIR»/src/dynlibsrc' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ subseqhash.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ intallocator.c intallocator.dy: In function ‘Wise2_show_allocator_status_IntAllocator’: intallocator.dy:216:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘unsigned int’ [-Wformat=] fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteinstreamedindex.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shadowseq.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shadowseqindex.c shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘unsigned int’ [-Wformat=] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsphandler.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspscaninterface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t {aka long int}’ [-Wformat=] fprintf(stderr,"START %d.%03du %d.%03ds \n", ^ hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t {aka long int}’ [-Wformat=] hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t {aka long int}’ [-Wformat=] fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", ^ hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t {aka long int}’ [-Wformat=] hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t {aka long int}’ [-Wformat=] fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", ^ hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t {aka long int}’ [-Wformat=] hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t {aka long int}’ [-Wformat=] fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", ^ hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t {aka long int}’ [-Wformat=] hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsplookupscan.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(stderr,"retrieved array with %d elements\n",current_oph); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment * {aka struct Wise2_HSPDatabaseSegment *}’ [-Wformat=] fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspscanruntime.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dnaindexcons.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[3]: Leaving directory '/«PKGBUILDDIR»/src/dynlibsrc' (cd external ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/«PKGBUILDDIR»/src/external' (cd mott; make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include" all) make[4]: Entering directory '/«PKGBUILDDIR»/src/external/mott' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c mott_api.c: In function ‘InitPvaluesMott’: mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration] free(freq0); ^ mott_api.c:64:3: warning: incompatible implicit declaration of built-in function ‘free’ mott_api.c:64:3: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘SW_PValueMott’: mott_api.c:104:7: warning: incompatible implicit declaration of built-in function ‘free’ free(freqA); ^ mott_api.c:104:7: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘KarlinAltschulStatistics2’: mott_api.c:144:5: warning: incompatible implicit declaration of built-in function ‘free’ free(h+hmin); ^ mott_api.c:144:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c:155:5: warning: incompatible implicit declaration of built-in function ‘free’ free(h+hmin); ^ mott_api.c:155:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘GetHistogram’: mott_api.c:179:16: warning: implicit declaration of function ‘calloc’ [-Wimplicit-function-declaration] h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function ‘calloc’ mott_api.c:179:16: note: include ‘’ or provide a declaration of ‘calloc’ mott_api.c: In function ‘PseudoResidueFrequencies2’: mott_api.c:207:12: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] freq[toupper(seq[n])]++; ^ mott_api.c: In function ‘RobinsonResidueFrequencies2’: mott_api.c:230:27: warning: incompatible implicit declaration of built-in function ‘calloc’ double *freq = (double*)calloc(256, sizeof(double)); ^ mott_api.c:230:27: note: include ‘’ or provide a declaration of ‘calloc’ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[4]: Leaving directory '/«PKGBUILDDIR»/src/external/mott' make[3]: Leaving directory '/«PKGBUILDDIR»/src/external' (cd socket ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/«PKGBUILDDIR»/src/socket' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ functionserver.c functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: functionserver.dy:129:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,9); ^ functionserver.dy:141:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,6); ^ functionserver.dy:183:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,5); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ functionclient.c functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’: functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types] connect(out->socket, &server, sizeof(server)); ^ In file included from functionclient.c:7:0: /usr/include/arm-linux-gnueabihf/sys/socket.h:137:12: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’ extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ anonobj.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ transferinterface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[3]: Leaving directory '/«PKGBUILDDIR»/src/socket' (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/«PKGBUILDDIR»/src/dnaindex' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’: kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); ^ kmer_assembly.dy:302:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); ^ kmer_assembly.dy:309:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); ^ kmer_assembly.dy: In function ‘Wise2_remove_sequence_label_KmerAssemblyLink’: kmer_assembly.dy:365:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘KmerAssemblyLink * {aka struct KmerAssemblyLink *}’ [-Wformat=] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ^ kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’: kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); ^ kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_glib_index.dy: In function ‘Wise2_retrieve_by_kmer_KmerGlibIndex’: kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); ^ kmer_glib_index.dy: In function ‘Wise2_insert_by_kmer_KmerGlibIndex’: kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); ^ kmer_glib_index.dy: In function ‘Wise2_retrieve_active_kmer_KmerGlibIndex’: kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ^ kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ^ kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t {aka long long int}’ [-Wformat=] kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ^ kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ^ kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); ^ kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of ‘Wise2_lift_backward_tangled_tail’ from incompatible pointer type [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^ In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.h:174:6: note: expected ‘int *’ but argument is of type ‘long int *’ void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ^ kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t {aka long long int}’ [-Wformat=] cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’: kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); ^ kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); ^ kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: kmer_assembly_error.dy:351:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’: compressed_protein_index.dy:223:10: warning: return makes integer from pointer without a cast [-Wint-conversion] return NULL; ^ make[3]: Leaving directory '/«PKGBUILDDIR»/src/dnaindex' (cd network ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/«PKGBUILDDIR»/src/network' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c wise_proteinindex_server.c: In function ‘show_version’: wise_proteinindex_server.c:28:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[3]: Leaving directory '/«PKGBUILDDIR»/src/network' (cd models ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory '/«PKGBUILDDIR»/src/models' cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c dnal.c: In function ‘show_version’: dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c pswdb.c: In function ‘show_version’: pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp," Compiled %s\n",COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. estwise.c: In function ‘show_version’: estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’: phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(name,10000,ifp); ^ In file included from /usr/include/stdio.h:936:0, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function ‘fgets’, inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:261:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function ‘Wise2_write_intron_desc’: genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] sprintf(buffer," Intron ??? ",in_number); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function ‘show_version’: genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ estwisedb.c: In function ‘show_version’: estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function ‘show_version’: genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’: est_evidence.dy:142:16: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] in->geu_free = free_EstEvidence; ^ cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function ‘show_version’: sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function ‘show_version’: pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c promoterwise.c: In function ‘show_version’: promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); ^ cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: motifmatrix.c:408:24: warning: assignment makes integer from pointer without a cast [-Wint-conversion] for(i=0;i dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make[2]: Leaving directory '/«PKGBUILDDIR»/debian/manpages.d' find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 108--108 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 197. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 8. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 204 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 5. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 206 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 207 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 208 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 209. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 214 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 4. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 15. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 16. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 217 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 218. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 20. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 20. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 7. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 228 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 9. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 230 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 232. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 233. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 234. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 235. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. Overfull \hbox (21.30891pt too wide) in paragraph at lines 236--237 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 238. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 388. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 39 0. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 2. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 394. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 396. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 398. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 399. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 400. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 401. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 02. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 09. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 410. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 1. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 412. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 3. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 414. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 415. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 416 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 422. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 423. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 4. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 25. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 426. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 432 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 433. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 434 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 440. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 1. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 442. LaTeX Warning: Reference `object_AlnBlock' on page 12 undefined on input line 4 50. LaTeX Warning: Reference `object_AlnColumn' on page 12 undefined on input line 452. LaTeX Warning: Reference `object_AlnUnit' on page 12 undefined on input line 45 4. LaTeX Warning: Reference `object_AlnSequence' on page 12 undefined on input lin e 456. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 463. Overfull \hbox (6.8248pt too wide) in paragraph at lines 474--481 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [12] LaTeX Warning: Reference `accessing_fields' on page 13 undefined on input line 512. [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 554. [14] LaTeX Warning: Reference `accessing_fields' on page 15 undefined on input line 622. [15] LaTeX Warning: Reference `object_AlnRange' on page 16 undefined on input line 6 51. LaTeX Warning: Reference `object_AlnRangeSet' on page 16 undefined on input lin e 653. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 660. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 687. [16] LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 740. LaTeX Warning: Reference `accessing_fields' on page 17 undefined on input line 747. [17] [18] [19] LaTeX Warning: Reference `object_cDNADB' on page 20 undefined on input line 883 . LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 923. [20] LaTeX Warning: Reference `object_CodonTable' on page 21 undefined on input line 1004. [21] [22] [23] [24] LaTeX Warning: Reference `accessing_fields' on page 25 undefined on input line 1212. [25] [26] [27] LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin e 1362. LaTeX Warning: Reference `accessing_fields' on page 28 undefined on input line 1390. [28] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1417--1418 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input line 1441. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 29 undefined o n input line 1443. LaTeX Warning: Reference `accessing_fields' on page 29 undefined on input line 1450. [29] LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1481. LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15 16. LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1523. [30] [31] LaTeX Warning: Reference `object_DBSearchImpl' on page 32 undefined on input li ne 1623. [32] LaTeX Warning: Reference `accessing_fields' on page 33 undefined on input line 1670. [33] LaTeX Warning: Reference `object_DnaMatrix' on page 34 undefined on input line 1735. LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l ine 1737. [34] LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1798. LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1811. [35] LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1843. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1850. [36] [37] LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19 47. LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l ine 1949. [38] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1988--1989 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 2037. [39] [40] LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line 2149. [41] LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 2167. Overfull \hbox (65.9032pt too wide) in paragraph at lines 2174--2175 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2191--2192 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2212. [43] LaTeX Warning: Reference `object_GenomicRegion' on page 44 undefined on input l ine 2297. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2304. [44] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2347--2348 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [45] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2400--2401 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2425--2426 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [46] [47] LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 2504. [48] LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line 2552. Overfull \hbox (32.9967pt too wide) in paragraph at lines 2591--2591 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [49] [50] [51] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2793--2794 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66585pt too wide) in paragraph at lines 2796--2797 []\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) [52] [53] [54] LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 292 9. LaTeX Warning: Reference `object_DataScore' on page 55 undefined on input line 2931. LaTeX Warning: Reference `object_DataEntry' on page 55 undefined on input line 2933. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2960. Overfull \hbox (30.97293pt too wide) in paragraph at lines 2970--2971 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [55] [56] [57] LaTeX Warning: Reference `accessing_fields' on page 58 undefined on input line 3161. [58] LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line 3187. LaTeX Warning: Reference `object_PackAln' on page 59 undefined on input line 32 28. [59] LaTeX Warning: Reference `object_PackAlnUnit' on page 60 undefined on input lin e 3230. LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3237. [60] LaTeX Warning: Reference `accessing_fields' on page 61 undefined on input line 3307. [61] [62] LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34 30. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3437. [63] LaTeX Warning: Reference `object_ProteinDB' on page 64 undefined on input line 3487. LaTeX Warning: Reference `accessing_fields' on page 64 undefined on input line 3544. [64] LaTeX Warning: Reference `object_RandomProteinDB' on page 65 undefined on input line 3589. LaTeX Warning: Reference `object_RandomDNADB' on page 65 undefined on input lin e 3591. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3598. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3619. [65] LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input line 3641. LaTeX Warning: Reference `object_RandomModel' on page 66 undefined on input lin e 3643. LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3681. [66] LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line 3696. LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3 712. LaTeX Warning: Reference `object_SequenceSet' on page 67 undefined on input lin e 3714. [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3778. [68] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3838--3839 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [69] [70] [71] [72] [73] [74] LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 4175. [75] [76] LaTeX Warning: Reference `object_SequenceDB' on page 77 undefined on input line 4264. LaTeX Warning: Reference `object_FileSource' on page 77 undefined on input line 4266. LaTeX Warning: Reference `accessing_fields' on page 77 undefined on input line 4293. [77] LaTeX Warning: Reference `accessing_fields' on page 78 undefined on input line 4354. LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4380. LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line 4382. [78] LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4389. LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4412. [79] LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin e 4481. LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 4488. Overfull \hbox (24.01358pt too wide) in paragraph at lines 4507--4514 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [80] LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line 4548. [81] LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4578. LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin e 4601. Overfull \hbox (62.7533pt too wide) in paragraph at lines 4608--4609 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [82] LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 4654. Overfull \hbox (335.96082pt too wide) in paragraph at lines 4670--4671 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [83] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4697--4698 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [84] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4731--4732 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [85] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4779--4780 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [86] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4800--4801 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input line 4829. LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l ine 4831. LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input line 4833. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4878. Overfull \hbox (1.40793pt too wide) in paragraph at lines 4892--4893 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4905. [88] LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4920. LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input line 4936. LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4943. [89] LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input line 4989. LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li ne 4991. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4998. Overfull \hbox (71.7832pt too wide) in paragraph at lines 5013--5014 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22557pt too wide) in paragraph at lines 5016--5017 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]estwise(qname,offset, target) [90] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5039--5040 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72548pt too wide) in paragraph at lines 5042--5043 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]genewise(qname,protof f,target) LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 5064. [91] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 92 undefined on input li ne 5106. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 92 undefined on input line 5108. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5115. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5151. [92] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5173--5174 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [93] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5216--5217 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in put line 5242. LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input line 5244. LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line 5246. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5253. Overfull \hbox (29.5499pt too wide) in paragraph at lines 5289--5290 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [95] LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5306. LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5319. Overfull \hbox (99.50298pt too wide) in paragraph at lines 5347--5348 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [96] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5372--5373 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5385--5386 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [97] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5406--5407 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5433--5434 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [98] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5454--5455 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5470--5473 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5477--5478 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [99] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5499--5500 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [100] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5522--5523 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l ine 5551. LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line 5558. [101] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5586--5587 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5593--5594 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5597--5598 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5668--5669 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [103] [104] LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu t line 5731. LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input line 5733. LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5774. [105] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5801--5802 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5821--5822 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09525pt too wide) in paragraph at lines 5824--5825 []\OT1/cmtt/m/n/10 $obj->force[]weighted[]local[]model(prob[]into[]model,ratio[ ]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5844--5845 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [106] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75575pt too wide) in paragraph at lines 5847--5848 []\OT1/cmtt/m/n/10 $obj->ThreeStateModel[]from[]half[]bit[]Sequence(mat,rm,gap, ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5871--5872 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5889. [107] [108] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (108 pages, 303731 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 108--108 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 232. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 235. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. Overfull \hbox (21.30891pt too wide) in paragraph at lines 236--237 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 238. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 388. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 25. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 434 . Overfull \hbox (6.8248pt too wide) in paragraph at lines 474--481 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1417--1418 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1988--1989 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [47] [48] [49] Overfull \hbox (65.9032pt too wide) in paragraph at lines 2174--2175 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2191--2192 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [50] [51] [52] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2347--2348 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [53] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2400--2401 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2425--2426 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [54] [55] [56] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2591--2591 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [57] [58] [59] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2793--2794 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66585pt too wide) in paragraph at lines 2796--2797 []\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) [60] [61] [62] Overfull \hbox (30.97293pt too wide) in paragraph at lines 2970--2971 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3838--3839 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (24.01358pt too wide) in paragraph at lines 4507--4514 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [88] [89] Overfull \hbox (62.7533pt too wide) in paragraph at lines 4608--4609 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [90] Overfull \hbox (335.96082pt too wide) in paragraph at lines 4670--4671 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [91] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4697--4698 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [92] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4731--4732 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [93] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4779--4780 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [94] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4800--4801 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [95] Overfull \hbox (1.40793pt too wide) in paragraph at lines 4892--4893 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [96] [97] Overfull \hbox (71.7832pt too wide) in paragraph at lines 5013--5014 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22557pt too wide) in paragraph at lines 5016--5017 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]estwise(qname,offset, target) [98] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5039--5040 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72548pt too wide) in paragraph at lines 5042--5043 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]genewise(qname,protof f,target) [99] [100] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5173--5174 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [101] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5216--5217 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5289--5290 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [103] Overfull \hbox (99.50298pt too wide) in paragraph at lines 5347--5348 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [104] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5372--5373 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5385--5386 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [105] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5406--5407 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5433--5434 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [106] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5454--5455 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5470--5473 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5477--5478 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [107] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5499--5500 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [108] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5522--5523 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) [109] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5586--5587 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5593--5594 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5597--5598 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [110] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5668--5669 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [111] [112] [113] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5801--5802 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5821--5822 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09525pt too wide) in paragraph at lines 5824--5825 []\OT1/cmtt/m/n/10 $obj->force[]weighted[]local[]model(prob[]into[]model,ratio[ ]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5844--5845 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [114] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75575pt too wide) in paragraph at lines 5847--5848 []\OT1/cmtt/m/n/10 $obj->ThreeStateModel[]from[]half[]bit[]Sequence(mat,rm,gap, ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5871--5872 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [115] [116] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (116 pages, 318251 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 76. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 252--256 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [7] [8] [9] [10] Overfull \hbox (48.74657pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [11] Overfull \hbox (269.24464pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [12] Overfull \hbox (22.4968pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [13] Overfull \hbox (59.24648pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [14] Overfull \hbox (48.74657pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [15] Overfull \hbox (80.24629pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 638--638 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 653--653 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [16] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [17] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 792--794 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [19] [20] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [22] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1014--1018 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1115--1115 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [23] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1115--1115 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [24] [25] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [26] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [27] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [28] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [29] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1341--1341 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [30] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1571--1571 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1571--1571 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [34] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1599--1599 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1633--1633 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1633--1633 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [36] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1726--1726 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1726--1726 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [37] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1848--1848 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1848--1848 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1848--1848 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [40] [41] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1910--1911 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1927--1927 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [42] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1954--1954 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1966--1966 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1966--1966 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [43] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2013--2013 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2013--2013 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [44] [45] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [46] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [47] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [48] Overfull \hbox (69.74638pt too wide) in paragraph at lines 2254--2254 []\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te mp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (95.99615pt too wide) in paragraph at lines 2254--2254 []\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na me,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2262--2262 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2262--2262 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [49] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2291--2291 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] [51] [52] [53] [54] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2527--2533 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [55] [56] [57] [58] [59] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2771--2775 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2791--2791 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2791--2791 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [60] [61] [62] (./dynamite.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (62 pages, 214158 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 252--256 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [9] [10] [11] [12] Overfull \hbox (48.74657pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [13] Overfull \hbox (269.24464pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [14] Overfull \hbox (22.4968pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 587--587 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [16] Overfull \hbox (48.74657pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [17] Overfull \hbox (80.24629pt too wide) in paragraph at lines 631--631 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 638--638 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 653--653 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [18] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 737--737 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 737--737 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [19] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 792--794 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [21] [22] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 941--941 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [24] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1014--1018 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1115--1115 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [25] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1115--1115 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [26] [27] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [28] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [29] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [30] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1334--1334 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [31] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1341--1341 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [32] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1378--1378 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1464--1464 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1571--1571 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1571--1571 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [36] [37] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1599--1599 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1633--1633 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1633--1633 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1726--1726 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1726--1726 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] [40] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1848--1848 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1848--1848 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [41] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1848--1848 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [42] [43] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1910--1911 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1927--1927 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [44] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1954--1954 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1966--1966 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1966--1966 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [45] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2013--2013 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2013--2013 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [46] [47] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [48] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [49] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] Overfull \hbox (69.74638pt too wide) in paragraph at lines 2254--2254 []\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te mp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (95.99615pt too wide) in paragraph at lines 2254--2254 []\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na me,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2254--2254 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2262--2262 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2262--2262 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [51] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2291--2291 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [52] [53] [54] [55] [56] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2527--2533 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [57] [58] [59] [60] [61] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2771--2775 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2791--2791 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2791--2791 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [62] [63] [64] (./dynamite.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (64 pages, 217702 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 109 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 112. Overfull \hbox (11.99689pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [5] Overfull \hbox (32.9967pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 296. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 5. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 4. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 454 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 65. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 2. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 2. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 12. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 707. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 899. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 964--967 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [22] [23] [24] [25] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1107--1108 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [26] LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11 80. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 120 9. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1267--1267 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1267--1267 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1275. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1311--1311 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1311--1311 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [30] [31] LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137 6. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 8. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 560. [37] [38] [39] [40] [41] [42] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (42 pages, 205912 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [6] Overfull \hbox (32.9967pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 205--205 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 707. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 964--967 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [23] [24] [25] [26] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1107--1108 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [27] [28] [29] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1267--1267 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1267--1267 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1311--1311 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1311--1311 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (43 pages, 208438 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:232: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:235: Warning: Undefined label: 'module_gwrap' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:388: Warning: Undefined label: 'module_gwrap' ./api.tex:425: Warning: Undefined label: 'module_codonmat' ./api.tex:434: Warning: Undefined label: 'module_dbimpl' ./api.tex:475: Warning: Application of '\'' on ',' failed ./api.tex:628: Warning: Application of '\'' on 't' failed ./api.tex:630: Warning: Application of '\'' on 'b' failed ./api.tex:632: Warning: Application of '\'' on 'b' failed ./api.tex:1641: Warning: Application of '\'' on 't' failed ./api.tex:1659: Warning: Application of '\'' on 't' failed ./api.tex:1881: Warning: Application of '\'' on '.' failed ./api.tex:2440: Warning: Application of '\'' on 'b' failed ./api.tex:2846: Warning: Application of '\'' on 'h' failed ./api.tex:2846: Warning: Application of '\'' on 't' failed ./api.tex:4434: Warning: Application of '\'' on '.' failed ./api.tex:4951: Warning: Application of '\'' on 'd' failed ./api.tex:4951: Warning: Application of '\'' on 'd' failed ./api.tex:5808: Warning: Application of '\'' on 'f' failed ./api.tex:5808: Warning: Application of '\'' on '[' failed ./api.tex:5829: Warning: Application of '\'' on 'f' failed ./api.tex:5829: Warning: Application of '\'' on '[' failed cd docs && hevea api.tex ./api.tex:232: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:235: Warning: Undefined label: 'module_gwrap' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:388: Warning: Undefined label: 'module_gwrap' ./api.tex:425: Warning: Undefined label: 'module_codonmat' ./api.tex:434: Warning: Undefined label: 'module_dbimpl' ./api.tex:475: Warning: Application of '\'' on ',' failed ./api.tex:628: Warning: Application of '\'' on 't' failed ./api.tex:630: Warning: Application of '\'' on 'b' failed ./api.tex:632: Warning: Application of '\'' on 'b' failed ./api.tex:1641: Warning: Application of '\'' on 't' failed ./api.tex:1659: Warning: Application of '\'' on 't' failed ./api.tex:1881: Warning: Application of '\'' on '.' failed ./api.tex:2440: Warning: Application of '\'' on 'b' failed ./api.tex:2846: Warning: Application of '\'' on 'h' failed ./api.tex:2846: Warning: Application of '\'' on 't' failed ./api.tex:4434: Warning: Application of '\'' on '.' failed ./api.tex:4951: Warning: Application of '\'' on 'd' failed ./api.tex:4951: Warning: Application of '\'' on 'd' failed ./api.tex:5808: Warning: Application of '\'' on 'f' failed ./api.tex:5808: Warning: Application of '\'' on '[' failed ./api.tex:5829: Warning: Application of '\'' on 'f' failed ./api.tex:5829: Warning: Application of '\'' on '[' failed cd docs && hevea dynamite.tex ./dynamite.tex:2617: Warning: Command not found: \+ ./dynamite.tex:2617: Warning: Command not found: \* ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2755: Warning: Application of '\"' on ')' failed ./dynamite.tex:2755: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2617: Warning: Command not found: \+ ./dynamite.tex:2617: Warning: Command not found: \* ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2755: Warning: Application of '\"' on ')' failed ./dynamite.tex:2755: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:240: Warning: \hbox ./wise2.tex:242: Warning: \hbox ./wise2.tex:244: Warning: \hbox ./wise2.tex:246: Warning: \hbox ./wise2.tex:248: Warning: \hbox ./wise2.tex:250: Warning: \hbox ./wise2.tex:252: Warning: \hbox ./wise2.tex:254: Warning: \hbox ./wise2.tex:262: Warning: \hbox ./wise2.tex:264: Warning: \hbox ./wise2.tex:266: Warning: \hbox ./wise2.tex:268: Warning: \hbox ./wise2.tex:270: Warning: \hbox ./wise2.tex:272: Warning: \hbox ./wise2.tex:274: Warning: \hbox ./wise2.tex:276: Warning: \hbox ./wise2.tex:707: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:711: Warning: Command not found: \leavevmode ./wise2.tex:903: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:240: Warning: \hbox ./wise2.tex:242: Warning: \hbox ./wise2.tex:244: Warning: \hbox ./wise2.tex:246: Warning: \hbox ./wise2.tex:248: Warning: \hbox ./wise2.tex:250: Warning: \hbox ./wise2.tex:252: Warning: \hbox ./wise2.tex:254: Warning: \hbox ./wise2.tex:262: Warning: \hbox ./wise2.tex:264: Warning: \hbox ./wise2.tex:266: Warning: \hbox ./wise2.tex:268: Warning: \hbox ./wise2.tex:270: Warning: \hbox ./wise2.tex:272: Warning: \hbox ./wise2.tex:274: Warning: \hbox ./wise2.tex:276: Warning: \hbox ./wise2.tex:707: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:711: Warning: Command not found: \leavevmode ./wise2.tex:903: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_auto_test make[1]: Entering directory '/«PKGBUILDDIR»' echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test make[1]: Leaving directory '/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f debian/wise.substvars rm -f debian/wise.*.debhelper rm -rf debian/wise/ dh_installdirs -a install -d debian/wise install -d debian/wise/usr/bin dh_auto_install -a dh_install -a cp --reflink=auto -a ./src/bin/dba debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/dnal debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/estwise debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/estwisedb debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/genewise debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/genewisedb debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/promoterwise debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/psw debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/pswdb debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/scanwise debian/wise/usr/bin/ cp --reflink=auto -a ./src/bin/scanwise_server debian/wise/usr/bin/ cp --reflink=auto -a ./src/models/genomewise debian/wise/usr/bin/ dh_installdocs -a install -d debian/wise/usr/share/doc/wise cp --reflink=auto -a README debian/wise/usr/share/doc/wise cp --reflink=auto -a debian/tests/run-unit-test debian/wise/usr/share/doc/wise chown -R 0:0 debian/wise/usr/share/doc chmod -R go=rX debian/wise/usr/share/doc chmod -R u\+rw debian/wise/usr/share/doc install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright dh_installchangelogs -a install -p -m0644 debian/changelog debian/wise/usr/share/doc/wise/changelog.Debian dh_installman -a install -d debian/wise/usr/share/man/man1/ install -p -m0644 debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -p -m0644 debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -p -m0644 debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -p -m0644 debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -p -m0644 debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -p -m0644 debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -p -m0644 debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -p -m0644 debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -p -m0644 debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -p -m0644 debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -p -m0644 debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -p -m0644 debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man --recode UTF-8 ./scanwise_server\.1 > scanwise_server\.1\.new chmod 644 scanwise_server.1.new mv -f scanwise_server.1.new scanwise_server.1 man --recode UTF-8 ./pswdb\.1 > pswdb\.1\.new chmod 644 pswdb.1.new mv -f pswdb.1.new pswdb.1 man --recode UTF-8 ./scanwise\.1 > scanwise\.1\.new chmod 644 scanwise.1.new mv -f scanwise.1.new scanwise.1 man --recode UTF-8 ./dnal\.1 > dnal\.1\.new chmod 644 dnal.1.new mv -f dnal.1.new dnal.1 man --recode UTF-8 ./estwise\.1 > estwise\.1\.new chmod 644 estwise.1.new mv -f estwise.1.new estwise.1 man --recode UTF-8 ./genewisedb\.1 > genewisedb\.1\.new chmod 644 genewisedb.1.new mv -f genewisedb.1.new genewisedb.1 man --recode UTF-8 ./promoterwise\.1 > promoterwise\.1\.new chmod 644 promoterwise.1.new mv -f promoterwise.1.new promoterwise.1 man --recode UTF-8 ./genomewise\.1 > genomewise\.1\.new chmod 644 genomewise.1.new mv -f genomewise.1.new genomewise.1 man --recode UTF-8 ./genewise\.1 > genewise\.1\.new chmod 644 genewise.1.new mv -f genewise.1.new genewise.1 man --recode UTF-8 ./psw\.1 > psw\.1\.new chmod 644 psw.1.new mv -f psw.1.new psw.1 man --recode UTF-8 ./dba\.1 > dba\.1\.new chmod 644 dba.1.new mv -f dba.1.new dba.1 man --recode UTF-8 ./estwisedb\.1 > estwisedb\.1\.new chmod 644 estwisedb.1.new mv -f estwisedb.1.new estwisedb.1 dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/wise chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 cd '/«PKGBUILDDIR»' dh_fixperms -a find debian/wise -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/wise ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise/usr/share/man debian/wise/usr/man/ debian/wise/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/lib/arm-linux-gnueabihf/perl5/5.22 debian/wise/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/wise -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/wise/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_strip -a 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: wise dh_strip debug symbol extraction: packages to act on: wise dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 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 strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise dh_makeshlibs -a rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a install -d debian/wise/DEBIAN dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal debian/wise/usr/bin/scanwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/pswdb debian/wise/usr/bin/estwise debian/wise/usr/bin/dba debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/genewise dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/wise.substvars echo misc:Pre-Depends= >> debian/wise.substvars dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 0644 debian/wise/DEBIAN/control chown 0:0 debian/wise/DEBIAN/control dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform armhf: wise dh_gencontrol debug symbol wrapper: packages to act on: wise dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package wise (pkgdir debian/wise, ddeb package dir debian/wise-dbgsym) dh_gencontrol debug symbol wrapper: building wise-dbgsym_2.4.1-18_armhf.ddeb dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-18_armhf.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile wise-dbgsym_2.4.1-18_armhf.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a (cd debian/wise >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 0644 debian/wise/DEBIAN/md5sums chown 0:0 debian/wise/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/wise .. INFO: pkgstriptranslations version 129 pkgstriptranslations: processing wise (in debian/wise); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/wise/DEBIAN/control, package wise, directory debian/wise pkgstripfiles: Truncating usr/share/doc/wise/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package wise ... pkgstripfiles: No PNG files. dpkg-deb: building package 'wise' in '../wise_2.4.1-18_armhf.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../wise_2.4.1-18_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build wise-2.4.1 dpkg-buildpackage: info: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160520-1727 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ wise_2.4.1-18_armhf.changes: ──────────────────────────── Format: 1.8 Date: Thu, 19 May 2016 21:53:30 +0000 Source: wise Binary: wise wise-doc wise-data Architecture: armhf Version: 2.4.1-18 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: wise - comparison of biopolymers, like DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Changes: wise (2.4.1-18) unstable; urgency=medium . * Team upload. * Make build reproducible. - Fix dates in manual .tex files. - Use stable order for API inputs. * Bump Standards-Version. * Enable full hardening. * Use secure Vcs-Browser. Checksums-Sha1: 947168ddc02ea14721babc9a1b067f077a02c247 2293470 wise-dbgsym_2.4.1-18_armhf.ddeb 4f6c34811d65998fc452c53da7bb8ef288f7ab0d 821562 wise_2.4.1-18_armhf.deb Checksums-Sha256: 3b49931c6646cedb537f82f171c133ab70629fc4390538968d87c420ba6fa6b7 2293470 wise-dbgsym_2.4.1-18_armhf.ddeb 6a6270ad9d0cd9bde53570de8d9002e8cd9b33d5f45193fc5881e0d4f0ae177e 821562 wise_2.4.1-18_armhf.deb Files: b0a6da2ce157abbc1243fa8e761ebee2 2293470 science extra wise-dbgsym_2.4.1-18_armhf.ddeb fe99d54924c0080c27286bf25dfe2447 821562 science optional wise_2.4.1-18_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ wise_2.4.1-18_armhf.deb ─────────────────────── new debian package, version 2.0. size 821562 bytes: control archive= 1981 bytes. 1798 bytes, 34 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-18 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6360 Depends: libc6 (>= 2.23), libglib2.0-0 (>= 2.12.0), wise-data (= 2.4.1-18) Suggests: wise-doc (= 2.4.1-18) Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, like DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. drwxr-xr-x root/root 0 2016-05-20 17:26 ./ drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/ drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/bin/ -rwxr-xr-x root/root 194124 2016-05-20 17:26 ./usr/bin/dba -rwxr-xr-x root/root 124420 2016-05-20 17:26 ./usr/bin/dnal -rwxr-xr-x root/root 1227752 2016-05-20 17:26 ./usr/bin/estwise -rwxr-xr-x root/root 1236028 2016-05-20 17:26 ./usr/bin/estwisedb -rwxr-xr-x root/root 1236024 2016-05-20 17:26 ./usr/bin/genewise -rwxr-xr-x root/root 1240180 2016-05-20 17:26 ./usr/bin/genewisedb -rwxr-xr-x root/root 214516 2016-05-20 17:26 ./usr/bin/genomewise -rwxr-xr-x root/root 226820 2016-05-20 17:26 ./usr/bin/promoterwise -rwxr-xr-x root/root 189956 2016-05-20 17:26 ./usr/bin/psw -rwxr-xr-x root/root 194124 2016-05-20 17:26 ./usr/bin/pswdb -rwxr-xr-x root/root 275972 2016-05-20 17:26 ./usr/bin/scanwise -rwxr-xr-x root/root 112120 2016-05-20 17:26 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/share/ drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/share/doc/wise/ -rw-r--r-- root/root 1973 2007-07-01 20:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 320 2013-09-12 08:58 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 1566 2016-05-20 17:27 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4219 2013-09-12 08:58 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 229 2014-09-23 11:53 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-20 17:26 ./usr/share/man/man1/ -rw-r--r-- root/root 847 2016-05-20 17:26 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2016-05-20 17:26 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2016-05-20 17:26 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2016-05-20 17:26 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2016-05-20 17:26 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2016-05-20 17:26 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2016-05-20 17:26 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2016-05-20 17:26 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2016-05-20 17:26 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2016-05-20 17:26 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2016-05-20 17:26 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2016-05-20 17:26 ./usr/share/man/man1/scanwise_server.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 115100 Build-Time: 676 Distribution: yakkety-proposed Host Architecture: armhf Install-Time: 242 Job: wise_2.4.1-18.dsc Machine Architecture: armhf Package: wise Package-Time: 924 Source-Version: 2.4.1-18 Space: 115100 Status: successful Version: 2.4.1-18 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160520-1727 Build needed 00:15:24, 115100k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9779061'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9779061/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9779061'] Unmounting chroot for build PACKAGEBUILD-9779061... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9779061'] Removing build PACKAGEBUILD-9779061