RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '588981-1558960', '/home/buildd/filecache-default/98a2b69f1174728d2ef8128d800d902108b5367f'] Synching the system clock with the buildd NTP service... 23 May 03:11:42 ntpdate[32230]: adjust time server 10.122.37.1 offset -0.000129 sec Unpacking chroot for build 588981-1558960 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '588981-1558960'] Mounting chroot for build 588981-1558960 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '588981-1558960', 'universe'] Attempting OGRE for universe in build-588981-1558960 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '588981-1558960', 'deb http://ftpmaster.internal/ubuntu intrepid main restricted universe'] Overriding sources.list in build-588981-1558960 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '588981-1558960'] Updating debian chroot for build 588981-1558960 Get:1 http://ftpmaster.internal intrepid Release.gpg [191B] Get:2 http://ftpmaster.internal intrepid Release [65.9kB] Get:3 http://ftpmaster.internal intrepid/main Packages [1153kB] Get:4 http://ftpmaster.internal intrepid/restricted Packages [1732B] Get:5 http://ftpmaster.internal intrepid/universe Packages [4230kB] Fetched 5450kB in 7s (762kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: perl perl-base perl-modules 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '588981-1558960', '--nolog', '--batch', '--archive=ubuntu', '--purpose=PRIMARY', '--dist=intrepid', '--comp=universe', 'poa_2.0+20060928-2.dsc'] Initiating build Automatic build of poa_2.0+20060928-2 on primero by sbuild/hppa 1.170.5 Build started at 20080523-0312 ****************************************************************************** poa_2.0+20060928-2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 5) Checking for already installed source dependencies... debhelper: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: netbase ifupdown update-inetd net-tools Use 'apt-get autoremove' to remove them. The following extra packages will be installed: bsdmainutils file gettext gettext-base groff-base html2text intltool-debian libmagic1 man-db po-debconf Suggested packages: vacation wamerican wordlist whois dh-make cvs gettext-doc groff less www-browser Recommended packages: curl wget lynx libcompress-zlib-perl libmail-box-perl libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libmagic1 man-db po-debconf 0 upgraded, 11 newly installed, 0 to remove and 3 not upgraded. Need to get 0B/6361kB of archives. After unpacking 20.1MB of additional disk space will be used. Selecting previously deselected package gettext-base. (Reading database ... 9565 files and directories currently installed.) Unpacking gettext-base (from .../gettext-base_0.17-2ubuntu1_hppa.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_6.1.10ubuntu2_hppa.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_4.24-2_hppa.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_4.24-2_hppa.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.18.1.1-20_hppa.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.2-1_hppa.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-3build2_hppa.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-2ubuntu1_hppa.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.13_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_7.0.8ubuntu1_all.deb) ... Setting up gettext-base (0.17-2ubuntu1) ... Setting up bsdmainutils (6.1.10ubuntu2) ... Setting up libmagic1 (4.24-2) ... Setting up file (4.24-2) ... Setting up groff-base (1.18.1.1-20) ... Setting up man-db (2.5.2-1) ... Building database of manual pages ... Setting up html2text (1.3.2a-3build2) ... Setting up gettext (0.17-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.13) ... Setting up debhelper (7.0.8ubuntu1) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.6.1-6ubuntu2 make_3.81-4 dpkg-dev_1.14.16.6ubuntu3 gcc-4.3_4.3.0-4ubuntu1 g++-4.3_4.3.0-4ubuntu1 binutils_2.18.50.20080509-0ubuntu1 libstdc++6_4.3.0-4ubuntu1 libstdc++6-4.3-dev_4.3.0-4ubuntu1 ------------------------------------------------------------------------------ dpkg-source: extracting poa in poa-2.0+20060928 dpkg-source: unpacking poa_2.0+20060928.orig.tar.gz dpkg-source: applying /home/buildd/build-588981-1558960/poa_2.0+20060928-2.diff.gz dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: source package poa dpkg-buildpackage: source version 2.0+20060928-2 dpkg-buildpackage: host architecture hppa /usr/bin/fakeroot debian/rules clean dh_testdir dh_testroot rm -f build-stamp [ ! -f Makefile ] || /usr/bin/make clean make[1]: Entering directory `/build/buildd/poa-2.0+20060928' rm -f align_score.o main.o black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o poa liblpo.a poa_doc libbflag.a make[1]: Leaving directory `/build/buildd/poa-2.0+20060928' dh_clean debian/rules build dh_testdir /usr/bin/make poa make[1]: Entering directory `/build/buildd/poa-2.0+20060928' gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o align_score.o align_score.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o main.o main.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o black_flag.o black_flag.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o seq_util.o seq_util.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o fasta_format.o fasta_format.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o msa_format.o msa_format.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o align_lpo2.o align_lpo2.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o align_lpo_po2.o align_lpo_po2.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o buildup_lpo.o buildup_lpo.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o lpo.o lpo.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o heaviest_bundle.o heaviest_bundle.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o lpo_format.o lpo_format.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o create_seq.o create_seq.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o remove_bundle.o remove_bundle.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o numeric_data.o numeric_data.c gcc -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -c -o stringptr.o stringptr.c rm -f liblpo.a ar rc liblpo.a black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o ranlib liblpo.a gcc -o poa align_score.o main.o -lm liblpo.a make[1]: Leaving directory `/build/buildd/poa-2.0+20060928' touch build-stamp /usr/bin/fakeroot debian/rules binary-arch dh_testdir /usr/bin/make poa make[1]: Entering directory `/build/buildd/poa-2.0+20060928' make[1]: `poa' is up to date. make[1]: Leaving directory `/build/buildd/poa-2.0+20060928' touch build-stamp dh_testdir dh_testroot dh_clean -k dh_installdirs dh_testdir dh_testroot dh_installchangelogs dh_installdocs README dh_installexamples multidom.seq dh_install dh_installman debian/poa.1 dh_link dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform hppa: poa dh_strip debug symbol extraction: packages to act on: poa dh_strip debug symbol extraction: ignored packages: pkgstriptranslations: processing control file: ./debian/poa-dbgsym/DEBIAN/control, package poa-dbgsym, directory ./debian/poa-dbgsym pkgstriptranslations: poa-dbgsym does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball dpkg-deb: building package `poa-dbgsym' in `../poa-dbgsym_2.0+20060928-2_hppa.ddeb'. dh_compress dh_fixperms dh_shlibdeps dpkg-shlibdeps: warning: debian/poa/usr/bin/poa shouldn't be linked with libm.so.6 (it uses none of its symbols). dh_gencontrol dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends} dh_md5sums dh_builddeb pkgstriptranslations: processing control file: ./debian/poa/DEBIAN/control, package poa, directory ./debian/poa pkgstriptranslations: poa does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball dpkg-deb: building package `poa' in `../poa_2.0+20060928-2_hppa.deb'. dpkg-genchanges -B -mUbuntu/hppa Build Daemon >../poa_2.0+20060928-2_hppa.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20080523-0313 Publishing debug debs. chroot-autobuild/build/buildd/poa_2.0+20060928-2_hppa.deb: new debian package, version 2.0. size 49128 bytes: control archive= 1129 bytes. 1008 bytes, 22 lines control 703 bytes, 11 lines md5sums Package: poa Version: 2.0+20060928-2 Architecture: hppa Maintainer: Debian-Med Packaging Team Installed-Size: 208 Depends: libc6 (>= 2.6.1-1) Suggests: blast2 Enhances: t-coffee Section: science Priority: optional Homepage: http://www.bioinformatics.ucla.edu/poa Description: Partial Order Alignment for multiple sequence alignment POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10-30 times faster than CLUSTALW. POA is published in Bioinformatics. 2004 Jul 10;20(10):1546-56. chroot-autobuild/build/buildd/poa_2.0+20060928-2_hppa.deb: drwxr-xr-x root/root 0 2008-05-23 03:13:39 ./ drwxr-xr-x root/root 0 2008-05-23 03:13:31 ./usr/ drwxr-xr-x root/root 0 2008-05-23 03:13:37 ./usr/bin/ -rwxr-xr-x root/root 116092 2008-05-23 03:13:37 ./usr/bin/poa drwxr-xr-x root/root 0 2008-05-23 03:13:33 ./usr/share/ drwxr-xr-x root/root 0 2008-05-23 03:13:33 ./usr/share/poa/ -rw-r--r-- root/root 3321 2004-03-12 08:10:08 ./usr/share/poa/blosum80.mat -rw-r--r-- root/root 3365 2004-03-12 06:08:14 ./usr/share/poa/blosum80_trunc.mat -rwxr-xr-x root/root 1284 2004-03-22 19:56:57 ./usr/share/poa/make_pscores.pl drwxr-xr-x root/root 0 2008-05-23 03:13:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2008-05-23 03:13:37 ./usr/share/doc/poa/ -rw-r--r-- root/root 366 2008-05-23 03:13:23 ./usr/share/doc/poa/NEWS.Debian.gz -rw-r--r-- root/root 4989 2004-03-22 20:01:59 ./usr/share/doc/poa/README.gz -rw-r--r-- root/root 574 2008-05-23 03:13:23 ./usr/share/doc/poa/README.Debian -rw-r--r-- root/root 1441 2008-05-23 03:13:23 ./usr/share/doc/poa/copyright drwxr-xr-x root/root 0 2008-05-23 03:13:32 ./usr/share/doc/poa/examples/ -rw-r--r-- root/root 2747 2004-03-12 05:28:11 ./usr/share/doc/poa/examples/multidom.seq -rw-r--r-- root/root 606 2008-05-23 03:13:23 ./usr/share/doc/poa/changelog.Debian.gz drwxr-xr-x root/root 0 2008-05-23 03:13:33 ./usr/share/man/ drwxr-xr-x root/root 0 2008-05-23 03:13:37 ./usr/share/man/man1/ -rw-r--r-- root/root 1969 2008-05-23 03:13:33 ./usr/share/man/man1/poa.1.gz poa_2.0+20060928-2_hppa.changes: Format: 1.7 Date: Fri, 21 Mar 2008 23:41:56 +0100 Source: poa Binary: poa Architecture: hppa Version: 2.0+20060928-2 Distribution: intrepid Urgency: low Maintainer: Ubuntu/hppa Build Daemon Changed-By: Andreas Tille Description: poa - Partial Order Alignment for multiple sequence alignment Changes: poa (2.0+20060928-2) unstable; urgency=low . [ Charles Plessy ] * debian/control: - Add Subversion repository URL to debian/control. - Moved the Homepage: field out from the package's description. - Enhances: t-coffee. . [ Nelson A. de Oliveira ] * Added watch file. . [ David Paleino ] * debian/poa.1 added - statically built * debian/control: - B-D updated - added myself to Uploaders - moved XS-Vcs-* to Vcs-* - Updated to Standards-Version 3.7.3 (no changes needed) * debian/rules: - statically build manpages (target poa.1 available) - minor changes . [ Andreas Tille ] * Added myself to uploaders Files: 4f3b3ec1faa98cca16f6d45abcb884ab 49128 science optional poa_2.0+20060928-2_hppa.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/poa-2.0+20060928 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --root=/home/buildd/build-588981-1558960/chroot-autobuild --purge po-debconf intltool-debian groff-base libmagic1 gettext file bsdmainutils html2text gettext-base man-db debhelper (Reading database ... 10629 files and directories currently installed.) Removing debhelper ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing groff-base ... Purging configuration files for groff-base ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... ****************************************************************************** Finished at 20080523-0313 Build needed 00:00:19, 1520k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '588981-1558960'] Scanning for processes to kill in build 588981-1558960... Scanning for processes to kill in build /home/buildd/build-588981-1558960/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '588981-1558960'] Unmounting chroot for build 588981-1558960... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '588981-1558960'] Removing build 588981-1558960