RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 2.6.38-1209-omap4 #22-Ubuntu SMP PREEMPT Wed Feb 22 16:33:32 UTC 2012 armv7l Buildd toolchain package versions: launchpad-buildd_113~0.IS.08.04 python-lpbuildd_113~0.IS.08.04 bzr_2.3.4-0ubuntu1. Syncing the system clock with the buildd NTP service... 7 May 13:09:50 ntpdate[31213]: adjust time server 10.211.37.1 offset -0.006478 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0', '/home/buildd/filecache-default/d8541851e63b8df21e521d59dce80e08c95e562c'] Unpacking chroot for build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0'] Mounting chroot for build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0', 'deb http://ftpmaster.internal/ubuntu quantal main universe'] Overriding sources.list in build-4424bd176c25bb5f9d6d77aef46b2f399dafcef0 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0', 'armel'] Updating debian chroot for build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0 Ign http://ftpmaster.internal quantal InRelease Get:1 http://ftpmaster.internal quantal Release.gpg [198 B] Get:2 http://ftpmaster.internal quantal Release [49.6 kB] Get:3 http://ftpmaster.internal quantal/main armel Packages [1293 kB] Get:4 http://ftpmaster.internal quantal/universe armel Packages [4816 kB] Get:5 http://ftpmaster.internal quantal/main TranslationIndex [74 B] Get:6 http://ftpmaster.internal quantal/universe TranslationIndex [75 B] Get:7 http://ftpmaster.internal quantal/main Translation-en [741 kB] Get:8 http://ftpmaster.internal quantal/universe Translation-en [3456 kB] Fetched 10.4 MB in 29s (352 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: debconf 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 146 kB of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! debconf Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ quantal/main debconf all 1.5.43ubuntu1 [146 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 146 kB in 0s (2426 kB/s) (Reading database ... 12119 files and directories currently installed.) Preparing to replace debconf 1.5.42ubuntu1 (using .../debconf_1.5.43ubuntu1_all.deb) ... Unpacking replacement debconf ... Setting up debconf (1.5.43ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0', 'armel', 'quantal', '--nolog', '--batch', '--archive=ubuntu', '--dist=quantal', '--purpose=PRIMARY', '--architecture=armel', '--comp=universe', 'cd-hit_4.6-2012-04-25-1.dsc'] Initiating build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0 with 2 jobs across 2 processor cores. Automatic build of cd-hit_4.6-2012-04-25-1 on nasl by sbuild/armel 1.170.5 Build started at 20120507-1311 ****************************************************************************** cd-hit_4.6-2012-04-25-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), mpi-default-dev, help2man Checking for already installed source dependencies... debhelper: missing mpi-default-dev: missing help2man: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper mpi-default-dev help2man Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor file gettext gettext-base groff-base html2text intltool-debian libcroco3 libgettextpo0 libibverbs-dev libibverbs1 liblocale-gettext-perl libmagic1 libopenmpi-dev libopenmpi1.3 libpipeline1 libtorque2 libunistring0 libxml2 man-db openmpi-common po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libgettextpo0 libibverbs-dev libibverbs1 liblocale-gettext-perl libmagic1 libopenmpi-dev libopenmpi1.3 libpipeline1 libtorque2 libunistring0 libxml2 man-db mpi-default-dev openmpi-common po-debconf 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 9033 kB of archives. After this operation, 28.8 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! liblocale-gettext-perl libmagic1 libpipeline1 libxml2 libcroco3 libunistring0 libgettextpo0 file bsdmainutils gettext-base groff-base man-db html2text gettext intltool-debian po-debconf dh-apparmor debhelper help2man libtorque2 openmpi-common libibverbs1 libibverbs-dev libopenmpi1.3 libopenmpi-dev mpi-default-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ quantal/main liblocale-gettext-perl armel 1.05-7build1 [18.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ quantal/main libmagic1 armel 5.11-1 [222 kB] Get:3 http://ftpmaster.internal/ubuntu/ quantal/main libpipeline1 armel 1.2.1-1 [20.7 kB] Get:4 http://ftpmaster.internal/ubuntu/ quantal/main libxml2 armel 2.7.8.dfsg-5.1ubuntu4 [548 kB] Get:5 http://ftpmaster.internal/ubuntu/ quantal/main libcroco3 armel 0.6.5-1 [82.2 kB] Get:6 http://ftpmaster.internal/ubuntu/ quantal/main libunistring0 armel 0.9.3-5 [394 kB] Get:7 http://ftpmaster.internal/ubuntu/ quantal/main libgettextpo0 armel 0.18.1.1-5ubuntu3 [99.4 kB] Get:8 http://ftpmaster.internal/ubuntu/ quantal/main file armel 5.11-1 [19.9 kB] Get:9 http://ftpmaster.internal/ubuntu/ quantal/main bsdmainutils armel 8.2.3ubuntu1 [194 kB] Get:10 http://ftpmaster.internal/ubuntu/ quantal/main gettext-base armel 0.18.1.1-5ubuntu3 [54.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ quantal/main groff-base armel 1.21-7 [923 kB] Get:12 http://ftpmaster.internal/ubuntu/ quantal/main man-db armel 2.6.1-2 [702 kB] Get:13 http://ftpmaster.internal/ubuntu/ quantal/main html2text armel 1.3.2a-15 [94.3 kB] Get:14 http://ftpmaster.internal/ubuntu/ quantal/main gettext armel 0.18.1.1-5ubuntu3 [1050 kB] Get:15 http://ftpmaster.internal/ubuntu/ quantal/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ quantal/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:17 http://ftpmaster.internal/ubuntu/ quantal/main dh-apparmor all 2.7.102-0ubuntu3 [9622 B] Get:18 http://ftpmaster.internal/ubuntu/ quantal/main debhelper all 9.20120419ubuntu2 [609 kB] Get:19 http://ftpmaster.internal/ubuntu/ quantal/main help2man armel 1.40.4ubuntu1 [54.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ quantal/universe libtorque2 armel 2.4.16+dfsg-1build1 [74.1 kB] Get:21 http://ftpmaster.internal/ubuntu/ quantal/universe openmpi-common all 1.4.3-2.1ubuntu3 [84.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ quantal/main libibverbs1 armel 1.1.5-1ubuntu1 [22.2 kB] Get:23 http://ftpmaster.internal/ubuntu/ quantal/main libibverbs-dev armel 1.1.5-1ubuntu1 [71.3 kB] Get:24 http://ftpmaster.internal/ubuntu/ quantal/universe libopenmpi1.3 armel 1.4.3-2.1ubuntu3 [1124 kB] Get:25 http://ftpmaster.internal/ubuntu/ quantal/universe libopenmpi-dev armel 1.4.3-2.1ubuntu3 [2317 kB] Get:26 http://ftpmaster.internal/ubuntu/ quantal/universe mpi-default-dev armel 1.0.1 [3646 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 9033 kB in 2s (3975 kB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12117 files and directories currently installed.) Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7build1_armel.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.11-1_armel.deb) ... Selecting previously unselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_armel.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1ubuntu4_armel.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.5-1_armel.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armel.deb) ... Selecting previously unselected package libgettextpo0. Unpacking libgettextpo0 (from .../libgettextpo0_0.18.1.1-5ubuntu3_armel.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armel.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3ubuntu1_armel.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5ubuntu3_armel.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armel.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armel.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5ubuntu3_armel.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2ubuntu1_all.deb) ... Selecting previously unselected package dh-apparmor. Unpacking dh-apparmor (from .../dh-apparmor_2.7.102-0ubuntu3_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419ubuntu2_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.40.4ubuntu1_armel.deb) ... Selecting previously unselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.16+dfsg-1build1_armel.deb) ... Selecting previously unselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.4.3-2.1ubuntu3_all.deb) ... Selecting previously unselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.5-1ubuntu1_armel.deb) ... Selecting previously unselected package libibverbs-dev. Unpacking libibverbs-dev (from .../libibverbs-dev_1.1.5-1ubuntu1_armel.deb) ... Selecting previously unselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.3-2.1ubuntu3_armel.deb) ... Selecting previously unselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.3-2.1ubuntu3_armel.deb) ... Selecting previously unselected package mpi-default-dev. Unpacking mpi-default-dev (from .../mpi-default-dev_1.0.1_armel.deb) ... Setting up liblocale-gettext-perl (1.05-7build1) ... Setting up libmagic1 (5.11-1) ... Setting up libpipeline1 (1.2.1-1) ... Setting up libxml2 (2.7.8.dfsg-5.1ubuntu4) ... Setting up libcroco3 (0.6.5-1) ... Setting up libunistring0 (0.9.3-5) ... Setting up libgettextpo0 (0.18.1.1-5ubuntu3) ... Setting up file (5.11-1) ... Setting up bsdmainutils (8.2.3ubuntu1) ... 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 gettext-base (0.18.1.1-5ubuntu3) ... Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.7.102-0ubuntu3) ... Setting up debhelper (9.20120419ubuntu2) ... Setting up help2man (1.40.4ubuntu1) ... Setting up libtorque2 (2.4.16+dfsg-1build1) ... Setting up openmpi-common (1.4.3-2.1ubuntu3) ... Setting up libibverbs1 (1.1.5-1ubuntu1) ... Setting up libibverbs-dev (1.1.5-1ubuntu1) ... Setting up libopenmpi1.3 (1.4.3-2.1ubuntu3) ... Setting up libopenmpi-dev (1.4.3-2.1ubuntu3) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode. Setting up mpi-default-dev (1.0.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu11 make_3.81-8.1ubuntu1 dpkg-dev_1.16.1.2ubuntu8 gcc-4.7_4.7.0-7ubuntu3 g++-4.7_4.7.0-7ubuntu3 binutils_2.22-6ubuntu1 libstdc++6-4.7-dev_4.7.0-7ubuntu3 libstdc++6_4.7.0-7ubuntu3 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Thu Apr 26 09:18:55 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./cd-hit_4.6-2012-04-25-1.dsc dpkg-source: info: extracting cd-hit in cd-hit-4.6-2012-04-25 dpkg-source: info: unpacking cd-hit_4.6-2012-04-25.orig.tar.gz dpkg-source: info: unpacking cd-hit_4.6-2012-04-25-1.debian.tar.gz dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying enable_help2man.patch dpkg-buildpackage: source package cd-hit dpkg-buildpackage: source version 4.6-2012-04-25-1 dpkg-source --before-build cd-hit-4.6-2012-04-25 dpkg-buildpackage: host architecture armel /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' rm -f *.o cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 make[1]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_clean debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_auto_build -- openmp=yes make[2]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-common.c++ -c cdhit-common.c++: In member function 'void SequenceDB::DoClustering(const Options&)': cdhit-common.c++:2990:66: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t {aka unsigned int}' [-Wformat] g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-utility.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit-est g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-2d.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit-2d g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est-2d.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit-est-2d g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-div.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit-div g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-454.c++ -c g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-Bsymbolic-functions -Wl,-z,relro -o cd-hit-454 make[2]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' make[1]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_auto_test /usr/bin/fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit make[2]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \ install -m 0755 $prog debian/cd-hit/usr/lib/cd-hit; \ done install -m 0755 *.pl debian/cd-hit/usr/lib/cd-hit; make[2]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' make[1]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' mkdir -p /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1/ help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='quickly group sequences' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit | \ sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cdhit.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='quickly group sequences in db1 or db2 format' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit-2d | \ sed -e 's/^cd-\(hit-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cdhit-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='run CD-HIT algorithm on RNA/DNA sequences' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit-est | \ sed -e 's/^cd-\(hit-est \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cdhit-est.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit-est-2d | \ sed -e 's/^cd-\(hit-est-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cdhit-est-2d.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit-2d-para.pl > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \ /build/buildd/cd-hit-4.6-2012-04-25/cd-hit-para.pl > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//cd-hit-para.1 # psi-cd-hit.pl is throwing some errors which are fixed using sed help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \ /build/buildd/cd-hit-4.6-2012-04-25/psi-cd-hit.pl | \ sed -e '/^Name "main::.*" used only once:/d' \ > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//psi-cd-hit.1 help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ /build/buildd/cd-hit-4.6-2012-04-25/psi-cd-hit-2d.pl > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d.1 # FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ? help2man --no-info --no-discard-stderr --version-string='4.6-2012-04-25' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ /build/buildd/cd-hit-4.6-2012-04-25/psi-cd-hit-2d-g1.pl > /build/buildd/cd-hit-4.6-2012-04-25/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d-g1.1 # No help output from # cd-hit-div.pl # clstr2tree.pl # clstr_merge.pl # clstr_merge_noorder.pl # clstr_reduce.pl # clstr_renumber.pl # clstr_rev.pl # clstr_sort_by.pl # clstr_sort_prot_by # make_multi_seq # psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors make[1]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_compress --exclude=.pdf make[1]: Leaving directory `/build/buildd/cd-hit-4.6-2012-04-25' dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform armel: cd-hit dh_strip debug symbol extraction: packages to act on: cd-hit dh_strip debug symbol extraction: ignored packages: dpkg-deb: building package `cd-hit-dbgsym' in `../cd-hit-dbgsym_4.6-2012-04-25-1_armel.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-div contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-454 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-2d contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 116 pkgstriptranslations: processing cd-hit (in debian/cd-hit); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/cd-hit/DEBIAN/control, package cd-hit, directory debian/cd-hit pkgstripfiles: PNG optimization for package cd-hit took 0 s dpkg-deb: warning: 'debian/cd-hit/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `cd-hit' in `../cd-hit_4.6-2012-04-25-1_armel.deb'. dpkg-genchanges -B -mUbuntu/armel Build Daemon >../cd-hit_4.6-2012-04-25-1_armel.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build cd-hit-4.6-2012-04-25 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120507-1314 Publishing debug debs. chroot-autobuild/build/buildd/cd-hit_4.6-2012-04-25-1_armel.deb: new debian package, version 2.0. size 681612 bytes: control archive= 2170 bytes. 1005 bytes, 18 lines control 3393 bytes, 51 lines md5sums Package: cd-hit Version: 4.6-2012-04-25-1 Architecture: armel Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1203 Depends: libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0), perl, mpi-default-bin Section: science Priority: optional Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Description: suite of programs designed to quickly group sequences cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information. chroot-autobuild/build/buildd/cd-hit_4.6-2012-04-25-1_armel.deb: drwxr-xr-x root/root 0 2012-05-07 13:14 ./ drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/ drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/bin/ drwxr-xr-x root/root 0 2012-05-07 13:13 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/lib/cd-hit/ -rwxr-xr-x root/root 1670 2012-05-07 13:13 ./usr/lib/cd-hit/make_multi_seq.pl -rwxr-xr-x root/root 11859 2012-05-07 13:13 ./usr/lib/cd-hit/cd-hit-para.pl -rwxr-xr-x root/root 1291 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_sort_prot_by.pl -rwxr-xr-x root/root 12596 2012-05-07 13:13 ./usr/lib/cd-hit/cd-hit-2d-para.pl -rwxr-xr-x root/root 112152 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit-div -rwxr-xr-x root/root 555 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_select_rep.pl -rwxr-xr-x root/root 1000 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_reduce.pl -rwxr-xr-x root/root 3668 2012-05-07 13:13 ./usr/lib/cd-hit/plot_2d.pl -rwxr-xr-x root/root 3199 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_merge.pl -rwxr-xr-x root/root 2162 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_merge_noorder.pl -rwxr-xr-x root/root 779 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_size_histogram.pl -rwxr-xr-x root/root 112152 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit -rwxr-xr-x root/root 57101 2012-05-07 13:13 ./usr/lib/cd-hit/psi-cd-hit-local.pl -rwxr-xr-x root/root 1209 2012-05-07 13:13 ./usr/lib/cd-hit/clstr2txt.pl -rwxr-xr-x root/root 112160 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit-est-2d -rwxr-xr-x root/root 1103 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_sql_tbl_sort.pl -rwxr-xr-x root/root 1160 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_reps_faa_rev.pl -rwxr-xr-x root/root 387 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_select.pl -rwxr-xr-x root/root 725 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_size_stat.pl -rwxr-xr-x root/root 2190 2012-05-07 13:13 ./usr/lib/cd-hit/plot_len1.pl -rwxr-xr-x root/root 112156 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit-2d -rwxr-xr-x root/root 952 2012-05-07 13:13 ./usr/lib/cd-hit/clstr2tree.pl -rwxr-xr-x root/root 196 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_renumber.pl -rwxr-xr-x root/root 112240 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit-454 -rwxr-xr-x root/root 3465 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_quality_eval.pl -rwxr-xr-x root/root 1620 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_rev.pl -rwxr-xr-x root/root 2328 2012-05-07 13:13 ./usr/lib/cd-hit/psi-cd-hit-2d.pl -rwxr-xr-x root/root 464 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_cut.pl -rwxr-xr-x root/root 2335 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_quality_eval_by_link.pl -rwxr-xr-x root/root 4503 2012-05-07 13:13 ./usr/lib/cd-hit/clstr2xml.pl -rwxr-xr-x root/root 1529 2012-05-07 13:13 ./usr/lib/cd-hit/psi-cd-hit-2d-g1.pl -rwxr-xr-x root/root 2028 2012-05-07 13:13 ./usr/lib/cd-hit/psi-cd-hit.pl -rwxr-xr-x root/root 2928 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_sql_tbl.pl -rwxr-xr-x root/root 554 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_rep.pl -rwxr-xr-x root/root 877 2012-05-07 13:13 ./usr/lib/cd-hit/cd-hit-div.pl -rwxr-xr-x root/root 806 2012-05-07 13:13 ./usr/lib/cd-hit/clstr_sort_by.pl -rwxr-xr-x root/root 112156 2012-05-07 13:14 ./usr/lib/cd-hit/cd-hit-est drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/share/ drwxr-xr-x root/root 0 2012-05-07 13:13 ./usr/share/doc-base/ -rw-r--r-- root/root 753 2011-12-22 08:06 ./usr/share/doc-base/cd-hit drwxr-xr-x root/root 0 2012-05-07 13:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/share/doc/cd-hit/ -rw-r--r-- root/root 303 2012-04-26 06:50 ./usr/share/doc/cd-hit/README.Debian -rw-r--r-- root/root 1982 2012-04-22 07:31 ./usr/share/doc/cd-hit/copyright -rw-r--r-- root/root 987 2012-04-26 09:03 ./usr/share/doc/cd-hit/changelog.Debian.gz -rw-r--r-- root/root 362533 2012-04-25 23:06 ./usr/share/doc/cd-hit/cdhit-user-guide.pdf drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-07 13:14 ./usr/share/man/man1/ -rw-r--r-- root/root 1691 2012-05-07 13:14 ./usr/share/man/man1/psi-cd-hit-2d.1.gz -rw-r--r-- root/root 1148 2012-05-07 13:14 ./usr/share/man/man1/cd-hit-2d-para.1.gz -rw-r--r-- root/root 1815 2012-05-07 13:14 ./usr/share/man/man1/cdhit-est.1.gz -rw-r--r-- root/root 1697 2012-05-07 13:14 ./usr/share/man/man1/psi-cd-hit-2d-g1.1.gz -rw-r--r-- root/root 1111 2012-05-07 13:14 ./usr/share/man/man1/cd-hit-para.1.gz -rw-r--r-- root/root 1657 2012-05-07 13:14 ./usr/share/man/man1/cdhit.1.gz -rw-r--r-- root/root 1919 2012-05-07 13:14 ./usr/share/man/man1/cdhit-est-2d.1.gz -rw-r--r-- root/root 1595 2012-05-07 13:14 ./usr/share/man/man1/psi-cd-hit.1.gz -rw-r--r-- root/root 1688 2012-05-07 13:14 ./usr/share/man/man1/cdhit-2d.1.gz lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_reduce -> ../lib/cd-hit/clstr_reduce.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cd-hit-div -> ../lib/cd-hit/cd-hit-div.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr2tree -> ../lib/cd-hit/clstr2tree.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cdhit-est -> ../lib/cd-hit/cd-hit-est lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_sort_by -> ../lib/cd-hit/clstr_sort_by.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/psi-cd-hit-local -> ../lib/cd-hit/psi-cd-hit-local.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cdhit -> ../lib/cd-hit/cd-hit lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_rev -> ../lib/cd-hit/clstr_rev.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/psi-cd-hit -> ../lib/cd-hit/psi-cd-hit.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cd-hit-para -> ../lib/cd-hit/cd-hit-para.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/make_multi_seq -> ../lib/cd-hit/make_multi_seq.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cdhit-2d -> ../lib/cd-hit/cd-hit-2d lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cdhit-est-2d -> ../lib/cd-hit/cd-hit-est-2d lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/psi-cd-hit-2d-g1 -> ../lib/cd-hit/psi-cd-hit-2d-g1.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_sort_prot_by -> ../lib/cd-hit/clstr_sort_prot_by.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_merge -> ../lib/cd-hit/clstr_merge.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/psi-cd-hit-2d -> ../lib/cd-hit/psi-cd-hit-2d.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/cd-hit-2d-para -> ../lib/cd-hit/cd-hit-2d-para.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_merge_noorder -> ../lib/cd-hit/clstr_merge_noorder.pl lrwxrwxrwx root/root 0 2012-05-07 13:14 ./usr/bin/clstr_renumber -> ../lib/cd-hit/clstr_renumber.pl cd-hit_4.6-2012-04-25-1_armel.changes: Format: 1.8 Date: Thu, 26 Apr 2012 07:54:23 +0200 Source: cd-hit Binary: cd-hit Architecture: armel Version: 4.6-2012-04-25-1 Distribution: quantal Urgency: low Maintainer: Ubuntu/armel Build Daemon Changed-By: Andreas Tille Description: cd-hit - suite of programs designed to quickly group sequences Changes: cd-hit (4.6-2012-04-25-1) unstable; urgency=low . * New upstream version incorporating the previous patches as well as the LaTeX source of the documentation * debian/patches/use-dpkg-buildflags.patch: Make sure hardening flags will really propagate * debian/{control,rules}: Use mpi version of cd-hit * README.Debian: Tell users that we are using mpi and they should ask for an alternative if needed * debian/*.1, debian/manpages: Deleted in favour of autogenerated manpages using help2man; Remark: the manually edited pages were slightly better regarding "SEE ALSO" and "AUTHORS" sections but it is better to auto-generate the pages to stay with changes of future versions * debian/rules: Use help2man 2 create manpages whereever possible * debian/patches/enable_help2man.patch: Fix some minor issues to get less error output in man pages Checksums-Sha1: cf8c07729907a7dc594f865172c4a3529677c1bb 681612 cd-hit_4.6-2012-04-25-1_armel.deb Checksums-Sha256: 9ca701880f181e6a501a805218b2b387b87f84cf2e5895302ff6d386327508e9 681612 cd-hit_4.6-2012-04-25-1_armel.deb Files: 39a00aeb94fa6cad1ee195dfe1f6cc2c 681612 science optional cd-hit_4.6-2012-04-25-1_armel.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120507-1314 Build needed 00:02:09, 10572k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0'] Scanning for processes to kill in build /home/buildd/build-4424bd176c25bb5f9d6d77aef46b2f399dafcef0/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0'] Unmounting chroot for build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '4424bd176c25bb5f9d6d77aef46b2f399dafcef0'] Removing build 4424bd176c25bb5f9d6d77aef46b2f399dafcef0