RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '1362496-2822891', '/home/buildd/filecache-default/6ca4616cb59ac2e24a82677a760ccbeb9269ee12'] Synching the system clock with the buildd NTP service... 24 Nov 07:54:18 ntpdate[27022]: adjust time server 10.211.37.1 offset 0.000286 sec Unpacking chroot for build 1362496-2822891 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '1362496-2822891'] Mounting chroot for build 1362496-2822891 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '1362496-2822891', 'universe'] Attempting OGRE for universe in build-1362496-2822891 No OGRE sources.list found. RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '1362496-2822891', 'deb http://ftpmaster.internal/ubuntu lucid main universe'] Overriding sources.list in build-1362496-2822891 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '1362496-2822891'] Updating debian chroot for build 1362496-2822891 Get:1 http://ftpmaster.internal lucid Release.gpg [189B] Get:2 http://ftpmaster.internal lucid Release [65.9kB] Get:3 http://ftpmaster.internal lucid/main Packages [1338kB] Get:4 http://ftpmaster.internal lucid/universe Packages [5077kB] Fetched 6481kB in 19s (330kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: diffutils The following packages have been kept back: pkg-create-dbgsym The following packages will be upgraded: base-files base-passwd binutils cpp-4.4 debconf debconf-i18n diff dpkg dpkg-dev g++-4.4 gcc-4.4 gcc-4.4-base initscripts insserv libacl1 libattr1 libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgcrypt11 libgdbm3 libgmp3c2 libgnutls26 libgomp1 libidn11 libkeyutils1 libsasl2-2 libsasl2-modules libselinux1 libsepol1 libstdc++6 libstdc++6-4.4-dev libtasn1-3 libtext-charwidth-perl libtext-iconv-perl libtimedate-perl libudev0 linux-libc-dev login make makedev passwd pkgbinarymangler python-minimal python2.6-minimal sed sysv-rc sysvinit-utils tar tzdata zlib1g 53 upgraded, 1 newly installed, 0 to remove and 1 not upgraded. Need to get 0B/28.6MB of archives. After this operation, 5292kB disk space will be freed. WARNING: The following packages cannot be authenticated! libc-dev-bin libc6-dev libc-bin libc6 linux-libc-dev libgomp1 cpp-4.4 gcc-4.4-base libgcc1 gcc-4.4 g++-4.4 libstdc++6-4.4-dev libstdc++6 libgmp3c2 zlib1g binutils libtext-iconv-perl libtext-charwidth-perl debconf-i18n debconf tzdata base-passwd base-files diffutils diff dpkg login sed tar python2.6-minimal python-minimal insserv libselinux1 libsepol1 sysvinit-utils sysv-rc passwd initscripts libattr1 libacl1 libudev0 libgcrypt11 libgdbm3 libtasn1-3 libgnutls26 libidn11 libkeyutils1 libsasl2-2 libsasl2-modules libtimedate-perl make makedev dpkg-dev pkgbinarymangler debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. (Reading database ... 10424 files and directories currently installed.) Preparing to replace libc-dev-bin 2.10.1-0ubuntu15 (using .../libc-dev-bin_2.10.1-3ubuntu1_armel.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.10.1-0ubuntu15 (using .../libc6-dev_2.10.1-3ubuntu1_armel.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.10.1-0ubuntu15 (using .../libc-bin_2.10.1-3ubuntu1_armel.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.10.1-3ubuntu1) ... (Reading database ... 10424 files and directories currently installed.) Preparing to replace libc6 2.10.1-0ubuntu15 (using .../libc6_2.10.1-3ubuntu1_armel.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.10.1-3ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10424 files and directories currently installed.) Preparing to replace linux-libc-dev 2.6.31-14.48 (using .../linux-libc-dev_2.6.32-5.6_armel.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace libgomp1 4.4.1-4ubuntu8 (using .../libgomp1_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement libgomp1 ... Preparing to replace cpp-4.4 4.4.1-4ubuntu8 (using .../cpp-4.4_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement cpp-4.4 ... Preparing to replace gcc-4.4-base 4.4.1-4ubuntu8 (using .../gcc-4.4-base_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement gcc-4.4-base ... Setting up gcc-4.4-base (4.4.2-1ubuntu4) ... (Reading database ... 10384 files and directories currently installed.) Preparing to replace libgcc1 1:4.4.1-4ubuntu8 (using .../libgcc1_1%3a4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.4.2-1ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10384 files and directories currently installed.) Preparing to replace gcc-4.4 4.4.1-4ubuntu8 (using .../gcc-4.4_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement gcc-4.4 ... Preparing to replace g++-4.4 4.4.1-4ubuntu8 (using .../g++-4.4_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement g++-4.4 ... Preparing to replace libstdc++6-4.4-dev 4.4.1-4ubuntu8 (using .../libstdc++6-4.4-dev_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement libstdc++6-4.4-dev ... Preparing to replace libstdc++6 4.4.1-4ubuntu8 (using .../libstdc++6_4.4.2-1ubuntu4_armel.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.4.2-1ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10394 files and directories currently installed.) Preparing to replace libgmp3c2 2:4.3.1+dfsg-1ubuntu3 (using .../libgmp3c2_2%3a4.3.1+dfsg-3_armel.deb) ... Unpacking replacement libgmp3c2 ... Preparing to replace zlib1g 1:1.2.3.3.dfsg-13ubuntu3 (using .../zlib1g_1%3a1.2.3.3.dfsg-15ubuntu1_armel.deb) ... Unpacking replacement zlib1g ... Setting up zlib1g (1:1.2.3.3.dfsg-15ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10394 files and directories currently installed.) Preparing to replace binutils 2.20-0ubuntu1 (using .../binutils_2.20-4ubuntu3_armel.deb) ... Unpacking replacement binutils ... Preparing to replace libtext-iconv-perl 1.7-1build1 (using .../libtext-iconv-perl_1.7-2_armel.deb) ... Unpacking replacement libtext-iconv-perl ... Setting up libtext-iconv-perl (1.7-2) ... (Reading database ... 10396 files and directories currently installed.) Preparing to replace libtext-charwidth-perl 0.04-5build1 (using .../libtext-charwidth-perl_0.04-6_armel.deb) ... Unpacking replacement libtext-charwidth-perl ... Setting up libtext-charwidth-perl (0.04-6) ... (Reading database ... 10396 files and directories currently installed.) Preparing to replace debconf-i18n 1.5.27ubuntu2 (using .../debconf-i18n_1.5.28ubuntu1_all.deb) ... Unpacking replacement debconf-i18n ... Setting up debconf-i18n (1.5.28ubuntu1) ... (Reading database ... 10396 files and directories currently installed.) Preparing to replace debconf 1.5.27ubuntu2 (using .../debconf_1.5.28ubuntu1_all.deb) ... Unpacking replacement debconf ... Setting up debconf (1.5.28ubuntu1) ... (Reading database ... 10382 files and directories currently installed.) Preparing to replace tzdata 2009o-1ubuntu2 (using .../tzdata_2009s-0ubuntu1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2009s-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Nov 24 07:55:42 UTC 2009. Universal Time is now: Tue Nov 24 07:55:42 UTC 2009. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 10385 files and directories currently installed.) Preparing to replace base-passwd 3.5.21 (using .../base-passwd_3.5.22_armel.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.22) ... (Reading database ... 10385 files and directories currently installed.) Preparing to replace base-files 5.0.0ubuntu7 (using .../base-files_5.0.0ubuntu8_armel.deb) ... Unpacking replacement base-files ... Setting up base-files (5.0.0ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously deselected package diffutils. (Reading database ... 10385 files and directories currently installed.) Unpacking diffutils (from .../diffutils_1%3a2.8.1-18_armel.deb) ... Replacing files in old package diff ... Setting up diffutils (1:2.8.1-18) ... (Reading database ... 10390 files and directories currently installed.) Preparing to replace diff 2.8.1-13 (using .../diff_1%3a2.8.1-18_all.deb) ... Unpacking replacement diff ... Setting up diff (1:2.8.1-18) ... (Reading database ... 10388 files and directories currently installed.) Preparing to replace dpkg 1.15.4ubuntu2 (using .../dpkg_1.15.4.1ubuntu1_armel.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.15.4.1ubuntu1) ... (Reading database ... 10388 files and directories currently installed.) Preparing to replace login 1:4.1.4.1-1ubuntu2 (using .../login_1%3a4.1.4.2-1ubuntu1_armel.deb) ... Unpacking replacement login ... Setting up login (1:4.1.4.2-1ubuntu1) ... Installing new version of config file /etc/pam.d/login ... Installing new version of config file /etc/securetty ... (Reading database ... 10388 files and directories currently installed.) Preparing to replace sed 4.2.1-1 (using .../archives/sed_4.2.1-4_armel.deb) ... Unpacking replacement sed ... Setting up sed (4.2.1-4) ... (Reading database ... 10388 files and directories currently installed.) Preparing to replace tar 1.22-1 (using .../archives/tar_1.22-2_armel.deb) ... Unpacking replacement tar ... Setting up tar (1.22-2) ... (Reading database ... 10388 files and directories currently installed.) Preparing to replace python2.6-minimal 2.6.4~rc2-0ubuntu1 (using .../python2.6-minimal_2.6.4-1ubuntu1_armel.deb) ... Unpacking replacement python2.6-minimal ... Setting up python2.6-minimal (2.6.4-1ubuntu1) ... (Reading database ... 10386 files and directories currently installed.) Preparing to replace python-minimal 2.6.4~rc1-0ubuntu1 (using .../python-minimal_2.6.4-0ubuntu2_all.deb) ... Unpacking replacement python-minimal ... Setting up python-minimal (2.6.4-0ubuntu2) ... (Reading database ... 10386 files and directories currently installed.) Preparing to replace insserv 1.12.0-11 (using .../insserv_1.12.0-14_armel.deb) ... Unpacking replacement insserv ... Setting up insserv (1.12.0-14) ... (Reading database ... 10387 files and directories currently installed.) Preparing to replace libselinux1 2.0.85-2ubuntu2 (using .../libselinux1_2.0.88-1_armel.deb) ... Unpacking replacement libselinux1 ... Setting up libselinux1 (2.0.88-1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10387 files and directories currently installed.) Preparing to replace libsepol1 2.0.37-1 (using .../libsepol1_2.0.39-1_armel.deb) ... Unpacking replacement libsepol1 ... Setting up libsepol1 (2.0.39-1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10387 files and directories currently installed.) Preparing to replace sysvinit-utils 2.87dsf-4ubuntu11 (using .../sysvinit-utils_2.87dsf-4ubuntu12_armel.deb) ... Unpacking replacement sysvinit-utils ... Setting up sysvinit-utils (2.87dsf-4ubuntu12) ... (Reading database ... 10387 files and directories currently installed.) Preparing to replace sysv-rc 2.87dsf-4ubuntu11 (using .../sysv-rc_2.87dsf-4ubuntu12_all.deb) ... Unpacking replacement sysv-rc ... Setting up sysv-rc (2.87dsf-4ubuntu12) ... (Reading database ... 10387 files and directories currently installed.) Preparing to replace passwd 1:4.1.4.1-1ubuntu2 (using .../passwd_1%3a4.1.4.2-1ubuntu1_armel.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.4.2-1ubuntu1) ... (Reading database ... 10384 files and directories currently installed.) Preparing to replace initscripts 2.87dsf-4ubuntu11 (using .../initscripts_2.87dsf-4ubuntu12_armel.deb) ... Unpacking replacement initscripts ... Setting up initscripts (2.87dsf-4ubuntu12) ... Installing new version of config file /etc/init.d/umountfs ... (Reading database ... 10383 files and directories currently installed.) Preparing to replace libattr1 1:2.4.43-3 (using .../libattr1_1%3a2.4.44-1_armel.deb) ... Unpacking replacement libattr1 ... Setting up libattr1 (1:2.4.44-1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10383 files and directories currently installed.) Preparing to replace libacl1 2.2.47-2 (using .../libacl1_2.2.48-1_armel.deb) ... Unpacking replacement libacl1 ... Setting up libacl1 (2.2.48-1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10383 files and directories currently installed.) Preparing to replace libudev0 147~-6 (using .../libudev0_147~-6.1_armel.deb) ... Unpacking replacement libudev0 ... Setting up libudev0 (147~-6.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 10383 files and directories currently installed.) Preparing to replace libgcrypt11 1.4.4-2ubuntu2 (using .../libgcrypt11_1.4.4-5ubuntu2_armel.deb) ... Unpacking replacement libgcrypt11 ... Preparing to replace libgdbm3 1.8.3-4 (using .../libgdbm3_1.8.3-8_armel.deb) ... Unpacking replacement libgdbm3 ... Preparing to replace libtasn1-3 2.2-1 (using .../libtasn1-3_2.3-1_armel.deb) ... Unpacking replacement libtasn1-3 ... Preparing to replace libgnutls26 2.8.3-2 (using .../libgnutls26_2.8.4-2_armel.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace libidn11 1.15-1 (using .../libidn11_1.15-2_armel.deb) ... Unpacking replacement libidn11 ... Preparing to replace libkeyutils1 1.2-10 (using .../libkeyutils1_1.2-12_armel.deb) ... Unpacking replacement libkeyutils1 ... Preparing to replace libsasl2-2 2.1.23.dfsg1-1ubuntu3 (using .../libsasl2-2_2.1.23.dfsg1-2ubuntu1_armel.deb) ... Unpacking replacement libsasl2-2 ... Preparing to replace libsasl2-modules 2.1.23.dfsg1-1ubuntu3 (using .../libsasl2-modules_2.1.23.dfsg1-2ubuntu1_armel.deb) ... Unpacking replacement libsasl2-modules ... Preparing to replace libtimedate-perl 1.1600-9 (using .../libtimedate-perl_1.1900-1_all.deb) ... Unpacking replacement libtimedate-perl ... Preparing to replace make 3.81-6 (using .../archives/make_3.81-7_armel.deb) ... Unpacking replacement make ... Preparing to replace makedev 2.3.1-88 (using .../makedev_2.3.1-89_all.deb) ... Unpacking replacement makedev ... Preparing to replace dpkg-dev 1.15.4ubuntu2 (using .../dpkg-dev_1.15.4.1ubuntu1_all.deb) ... Unpacking replacement dpkg-dev ... Preparing to replace pkgbinarymangler 63 (using .../pkgbinarymangler_64_all.deb) ... Unpacking replacement pkgbinarymangler ... Setting up libc-dev-bin (2.10.1-3ubuntu1) ... Setting up linux-libc-dev (2.6.32-5.6) ... Setting up libc6-dev (2.10.1-3ubuntu1) ... Setting up libgomp1 (4.4.2-1ubuntu4) ... Setting up libgmp3c2 (2:4.3.1+dfsg-3) ... Setting up cpp-4.4 (4.4.2-1ubuntu4) ... Setting up binutils (2.20-4ubuntu3) ... Setting up gcc-4.4 (4.4.2-1ubuntu4) ... Setting up libgcrypt11 (1.4.4-5ubuntu2) ... Setting up libgdbm3 (1.8.3-8) ... Setting up libtasn1-3 (2.3-1) ... Setting up libgnutls26 (2.8.4-2) ... Setting up libidn11 (1.15-2) ... Setting up libkeyutils1 (1.2-12) ... Setting up libtimedate-perl (1.1900-1) ... Setting up make (3.81-7) ... Setting up makedev (2.3.1-89) ... Setting up dpkg-dev (1.15.4.1ubuntu1) ... Setting up pkgbinarymangler (64) ... Setting up g++-4.4 (4.4.2-1ubuntu4) ... Setting up libsasl2-modules (2.1.23.dfsg1-2ubuntu1) ... Setting up libsasl2-2 (2.1.23.dfsg1-2ubuntu1) ... Setting up libstdc++6-4.4-dev (4.4.2-1ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '1362496-2822891', '--nolog', '--batch', '--archive=ubuntu', '--purpose=PRIMARY', '--dist=lucid', '--comp=universe', 'theseus_1.4.3-2.dsc'] Initiating build 1362496-2822891 with 0 processor cores. Automatic build of theseus_1.4.3-2 on imbe by sbuild/armel 1.170.5 Build started at 20091124-0756 ****************************************************************************** theseus_1.4.3-2.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7.1), quilt, libgsl0-dev, liblapack-dev, libtool Checking for already installed source dependencies... debhelper: missing quilt: missing libgsl0-dev: missing liblapack-dev: missing libtool: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper quilt libgsl0-dev liblapack-dev libtool Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils diffstat file gettext gettext-base groff-base html2text intltool-debian libblas-dev libblas3gf libcroco3 libgfortran3 libglib2.0-0 libgsl0ldbl liblapack3gf libmagic1 libpcre3 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html libtool-doc autoconf automaken gfortran fortran95-compiler gcj less www-browser libmail-box-perl procmail graphviz Recommended packages: curl wget lynx cvs libglib2.0-data shared-mime-info libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libblas-dev libblas3gf libcroco3 libgfortran3 libglib2.0-0 libgsl0-dev libgsl0ldbl liblapack-dev liblapack3gf libmagic1 libpcre3 libtool libxml2 man-db po-debconf quilt 0 upgraded, 26 newly installed, 0 to remove and 1 not upgraded. Need to get 1867kB/14.5MB of archives. After this operation, 51.7MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libmagic1 file libpcre3 libglib2.0-0 libxml2 bsdmainutils gettext-base groff-base man-db autotools-dev html2text libcroco3 gettext intltool-debian po-debconf debhelper diffstat libgfortran3 libblas3gf libblas-dev libgsl0ldbl libgsl0-dev liblapack3gf liblapack-dev libtool quilt Authentication warning overridden. Get:1 http://ftpmaster.internal lucid/main libgsl0ldbl 1.13+dfsg-1 [796kB] Get:2 http://ftpmaster.internal lucid/main libgsl0-dev 1.13+dfsg-1 [1071kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1867kB in 0s (5296kB/s) Selecting previously deselected package libmagic1. (Reading database ... 10398 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_5.03-1ubuntu1_armel.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.03-1ubuntu1_armel.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_7.8-3_armel.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.22.2-0ubuntu1_armel.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.5.dfsg-1ubuntu1_armel.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.0.1ubuntu1_armel.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.17-8ubuntu2_armel.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.20.1-6_armel.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.6-4_armel.deb) ... Selecting previously deselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20090611.1_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-14_armel.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.17-8ubuntu2_armel.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_1.0.16_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_7.4.3ubuntu2_all.deb) ... Selecting previously deselected package diffstat. Unpacking diffstat (from .../diffstat_1.47-1_armel.deb) ... Selecting previously deselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.4.2-1ubuntu4_armel.deb) ... Selecting previously deselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2-2_armel.deb) ... Selecting previously deselected package libblas-dev. Unpacking libblas-dev (from .../libblas-dev_1.2-2_armel.deb) ... Selecting previously deselected package libgsl0ldbl. Unpacking libgsl0ldbl (from .../libgsl0ldbl_1.13+dfsg-1_armel.deb) ... Selecting previously deselected package libgsl0-dev. Unpacking libgsl0-dev (from .../libgsl0-dev_1.13+dfsg-1_armel.deb) ... Selecting previously deselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.2.1-2_armel.deb) ... Selecting previously deselected package liblapack-dev. Unpacking liblapack-dev (from .../liblapack-dev_3.2.1-2_armel.deb) ... Selecting previously deselected package libtool. Unpacking libtool (from .../libtool_2.2.6a-4_armel.deb) ... Selecting previously deselected package quilt. Unpacking quilt (from .../quilt_0.46-8ubuntu1_all.deb) ... Setting up libmagic1 (5.03-1ubuntu1) ... Setting up file (5.03-1ubuntu1) ... Setting up libpcre3 (7.8-3) ... Setting up libglib2.0-0 (2.22.2-0ubuntu1) ... Setting up libxml2 (2.7.5.dfsg-1ubuntu1) ... Setting up bsdmainutils (8.0.1ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. Setting up gettext-base (0.17-8ubuntu2) ... Setting up groff-base (1.20.1-6) ... Setting up man-db (2.5.6-4) ... Building database of manual pages ... ... skipping, since this is a buildd Setting up autotools-dev (20090611.1) ... Setting up html2text (1.3.2a-14) ... Setting up libcroco3 (0.6.2-1) ... Setting up gettext (0.17-8ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16) ... Setting up debhelper (7.4.3ubuntu2) ... Setting up diffstat (1.47-1) ... Setting up libgfortran3 (4.4.2-1ubuntu4) ... Setting up libblas3gf (1.2-2) ... Setting up libblas-dev (1.2-2) ... update-alternatives: using /usr/lib/libblas.so to provide /usr/lib/libblas-3gf.so (libblas-3gf.so) in auto mode. Setting up libgsl0ldbl (1.13+dfsg-1) ... Setting up libgsl0-dev (1.13+dfsg-1) ... Setting up liblapack3gf (3.2.1-2) ... Setting up liblapack-dev (3.2.1-2) ... update-alternatives: using /usr/lib/liblapack.so to provide /usr/lib/liblapackgf-3.so (liblapackgf-3.so) in auto mode. Setting up libtool (2.2.6a-4) ... Setting up quilt (0.46-8ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.10.1-3ubuntu1 make_3.81-7 dpkg-dev_1.15.4.1ubuntu1 g++-4.4_4.4.2-1ubuntu4 gcc-4.4_4.4.2-1ubuntu4 binutils_2.20-4ubuntu3 libstdc++6_4.4.2-1ubuntu4 libstdc++6-4.4-dev_4.4.2-1ubuntu4 ------------------------------------------------------------------------------ gpg: Signature made Thu Sep 3 07:53:21 2009 BST using DSA key ID C09FD35A gpg: Can't check signature: public key not found dpkg-source: extracting theseus in theseus-1.4.3 dpkg-source: info: unpacking theseus_1.4.3.orig.tar.gz dpkg-source: info: applying theseus_1.4.3-2.diff.gz dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: source package theseus dpkg-buildpackage: source version 1.4.3-2 dpkg-buildpackage: host architecture armel /usr/bin/fakeroot debian/rules clean dh --with quilt clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/theseus-1.4.3' dh_quilt_patch Applying patch 00-makefile.patch patching file Makefile Applying patch 200-make.inc.patch patching file make.inc Applying patch 99-theseus_align.sh.patch patching file theseus_align Applying patch 10_kbsd.patch patching file distfit.h patching file theseus.h Now at patch 10_kbsd.patch dh_auto_clean make[2]: Entering directory `/build/buildd/theseus-1.4.3' find . -name '*.[oa]' -exec rm -f {} \; rm -f theseus &> /dev/null make[2]: Leaving directory `/build/buildd/theseus-1.4.3' make[1]: Leaving directory `/build/buildd/theseus-1.4.3' dh_quilt_unpatch Removing patch 10_kbsd.patch Restoring theseus.h Restoring distfit.h Removing patch 99-theseus_align.sh.patch Restoring theseus_align Removing patch 200-make.inc.patch Restoring make.inc Removing patch 00-makefile.patch Restoring Makefile No patches applied dh_clean debian/rules build dh --with quilt build dh_testdir dh_quilt_patch Applying patch 00-makefile.patch patching file Makefile Applying patch 200-make.inc.patch patching file make.inc Applying patch 99-theseus_align.sh.patch patching file theseus_align Applying patch 10_kbsd.patch patching file distfit.h patching file theseus.h Now at patch 10_kbsd.patch dh_auto_configure dh_auto_build make[1]: Entering directory `/build/buildd/theseus-1.4.3' ( cd libdistfit; make && cp libdistfit.a ../lib ) make[2]: Entering directory `/build/buildd/theseus-1.4.3/libdistfit' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c bimultinom.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c statistics.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c beta_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c betasym_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c binomial_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c cauchy_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c chi_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c chisqr_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c chisqrgen_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c EVD_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c exp_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c gamma_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c invchisqr_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c invgamma_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c invgauss_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c laplace_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c logistic_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c lognormal_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c maxwell_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c negbinom_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c normal_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pareto_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c recinvgauss_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c uniform_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c vonmises_dist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c weibull_dist.c ar -rvs libdistfit.a bimultinom.o statistics.o beta_dist.o betasym_dist.o binomial_dist.o cauchy_dist.o chi_dist.o chisqr_dist.o chisqrgen_dist.o EVD_dist.o exp_dist.o gamma_dist.o invchisqr_dist.o invgamma_dist.o invgauss_dist.o laplace_dist.o logistic_dist.o lognormal_dist.o maxwell_dist.o negbinom_dist.o normal_dist.o pareto_dist.o recinvgauss_dist.o uniform_dist.o vonmises_dist.o weibull_dist.o ar: creating libdistfit.a a - bimultinom.o a - statistics.o a - beta_dist.o a - betasym_dist.o a - binomial_dist.o a - cauchy_dist.o a - chi_dist.o a - chisqr_dist.o a - chisqrgen_dist.o a - EVD_dist.o a - exp_dist.o a - gamma_dist.o a - invchisqr_dist.o a - invgamma_dist.o a - invgauss_dist.o a - laplace_dist.o a - logistic_dist.o a - lognormal_dist.o a - maxwell_dist.o a - negbinom_dist.o a - normal_dist.o a - pareto_dist.o a - recinvgauss_dist.o a - uniform_dist.o a - vonmises_dist.o a - weibull_dist.o ranlib libdistfit.a make[2]: Leaving directory `/build/buildd/theseus-1.4.3/libdistfit' ( cd libDLTutils; make && cp libDLTutils.a ../lib ) make[2]: Entering directory `/build/buildd/theseus-1.4.3/libDLTutils' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c DLTutils.c ar -rvs libDLTutils.a DLTutils.o ar: creating libDLTutils.a a - DLTutils.o ranlib libDLTutils.a make[2]: Leaving directory `/build/buildd/theseus-1.4.3/libDLTutils' ( cd libmsa; make && cp libmsa.a ../lib ) make[2]: Entering directory `/build/buildd/theseus-1.4.3/libmsa' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c msa.c msa.c: In function 'getmsa': msa.c:80: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c: In function 'isnexdist': msa.c:147: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c: In function 'ismsf': msa.c:181: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c: In function 'readaln': msa.c:1306: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c:1369: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c:1396: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c: In function 'readphylip': msa.c:2088: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c:2110: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result msa.c: In function 'readphylipd': msa.c:2155: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result ar -rvs libmsa.a msa.o ar: creating libmsa.a a - msa.o ranlib libmsa.a make[2]: Leaving directory `/build/buildd/theseus-1.4.3/libmsa' ( cd libdltmath; make && cp libdltmath.a ../lib ) make[2]: Entering directory `/build/buildd/theseus-1.4.3/libdltmath' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c ludcmp.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c MatUtils.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c Mat3Utils.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c Mat4Utils.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c VecUtils.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c ncbi_math.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c specfunc.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c RegGamma.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c quicksort.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c myrandom.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c integrate.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c lapack_dlt.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c eigen.c ar -rvs libdltmath.a ludcmp.o MatUtils.o Mat3Utils.o Mat4Utils.o VecUtils.o ncbi_math.o specfunc.o RegGamma.o quicksort.o myrandom.o integrate.o lapack_dlt.o eigen.o ar: creating libdltmath.a a - ludcmp.o a - MatUtils.o a - Mat3Utils.o a - Mat4Utils.o a - VecUtils.o a - ncbi_math.o a - specfunc.o a - RegGamma.o a - quicksort.o a - myrandom.o a - integrate.o a - lapack_dlt.o a - eigen.o ranlib libdltmath.a make[2]: Leaving directory `/build/buildd/theseus-1.4.3/libdltmath' ( cd libdssplite; make && cp libdssplite.a ../lib ) make[2]: Entering directory `/build/buildd/theseus-1.4.3/libdssplite' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c dssplite.c ar -rvs libdssplite.a dssplite.o ar: creating libdssplite.a a - dssplite.o ranlib libdssplite.a make[2]: Leaving directory `/build/buildd/theseus-1.4.3/libdssplite' gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c CovMat.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c DistMat.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c Embed.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c Error.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c FragCoords.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c FragDist.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c HierarchVars.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c LedoitWolf.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c lodmats.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c MultiPose.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c MultiPose2MSA.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c MultiPoseMix.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c PCAstats.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pdbIO.c pdbIO.c: In function 'ReadBinPDBCoordsArray': pdbIO.c:1670: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1680: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1681: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c: In function 'ReadBinPDBCoords': pdbIO.c:1741: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1744: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1745: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1747: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1749: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1750: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1751: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1752: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1753: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1754: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1755: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1756: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1757: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1758: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1759: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1760: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1762: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1763: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1764: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1765: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1766: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1767: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c: In function 'ReadBinMatrix': pdbIO.c:1785: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1786: warning: ignoring return value of 'fread', declared with attribute warn_unused_result pdbIO.c:1787: warning: ignoring return value of 'fread', declared with attribute warn_unused_result gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pdbMalloc.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pdbStats.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pdbUtils.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c QuarticHornFrag.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c RandCoords.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c pdbSSM.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c ProcLAPACKSVDOcc.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c ProcLAPACKSVD.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c ProcJacobiSVD.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c Kabsch.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c termcol.c gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c theseuslib.c ar -rvs libtheseus.a CovMat.o DistMat.o Embed.o Error.o FragCoords.o FragDist.o HierarchVars.o LedoitWolf.o lodmats.o MultiPose.o MultiPose2MSA.o MultiPoseMix.o PCAstats.o pdbIO.o pdbMalloc.o pdbStats.o pdbUtils.o QuarticHornFrag.o RandCoords.o pdbSSM.o ProcLAPACKSVDOcc.o ProcLAPACKSVD.o ProcJacobiSVD.o Kabsch.o termcol.o theseuslib.o ar: creating libtheseus.a a - CovMat.o a - DistMat.o a - Embed.o a - Error.o a - FragCoords.o a - FragDist.o a - HierarchVars.o a - LedoitWolf.o a - lodmats.o a - MultiPose.o a - MultiPose2MSA.o a - MultiPoseMix.o a - PCAstats.o a - pdbIO.o a - pdbMalloc.o a - pdbStats.o a - pdbUtils.o a - QuarticHornFrag.o a - RandCoords.o a - pdbSSM.o a - ProcLAPACKSVDOcc.o a - ProcLAPACKSVD.o a - ProcJacobiSVD.o a - Kabsch.o a - termcol.o a - theseuslib.o mv libtheseus.a lib/libtheseus.a ranlib lib/libtheseus.a gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -c theseus.c theseus.c: In function 'ConvertLele': theseus.c:1130: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result gcc -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wall -pedantic -std=c99 -DNDEBUG -Wall -pedantic -std=c99 -L./lib theseus.o CovMat.o DistMat.o Embed.o Error.o FragCoords.o FragDist.o HierarchVars.o LedoitWolf.o lodmats.o MultiPose.o MultiPose2MSA.o MultiPoseMix.o PCAstats.o pdbIO.o pdbMalloc.o pdbStats.o pdbUtils.o QuarticHornFrag.o RandCoords.o pdbSSM.o ProcLAPACKSVDOcc.o ProcLAPACKSVD.o ProcJacobiSVD.o Kabsch.o termcol.o theseuslib.o -Llib -ldistfit -lgsl -lmsa -ldssplite -ldltmath -lDLTutils -L/usr/lib/atlas -llapack -lpthread -lm -lc -o theseus make[1]: Leaving directory `/build/buildd/theseus-1.4.3' dh_auto_test /usr/bin/fakeroot debian/rules binary-arch dh --with quilt binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/theseus-1.4.3' echo "Do not call make install, use dh_install instead" Do not call make install, use dh_install instead make[1]: Leaving directory `/build/buildd/theseus-1.4.3' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a 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_bugfiles -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform armel: theseus dh_strip debug symbol extraction: packages to act on: theseus dh_strip debug symbol extraction: ignored packages: WARNING: not running pkgbinarymangler for this package, as requested dpkg-deb: building package `theseus-dbgsym' in `../theseus-dbgsym_1.4.3-2_armel.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a pkgstriptranslations: processing control file: ./debian/theseus/DEBIAN/control, package theseus, directory ./debian/theseus pkgstriptranslations: theseus does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgstriptranslations: static tarball already exists pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " dpkg-deb: warning: 'debian/theseus/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warnings about the control file(s) dpkg-deb: building package `theseus' in `../theseus_1.4.3-2_armel.deb'. dpkg-genchanges -B -mUbuntu/armel Build Daemon >../theseus_1.4.3-2_armel.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 20091124-0803 Publishing debug debs. chroot-autobuild/build/buildd/theseus_1.4.3-2_armel.deb: new debian package, version 2.0. size 1147110 bytes: control archive= 1770 bytes. 1153 bytes, 23 lines control 2513 bytes, 33 lines md5sums Package: theseus Version: 1.4.3-2 Architecture: armel Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1624 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), liblapack3gf | liblapack.so.3gf | libatlas3gf-base Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign Section: science Priority: optional Homepage: http://www.theseus3d.org Description: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By down-weighting variable regions of the superposition and by correcting for correlations among atoms, the ML superposition method produces very accurate structural alignments. . When macromolecules with different residue sequences are superimposed, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data. chroot-autobuild/build/buildd/theseus_1.4.3-2_armel.deb: drwxr-xr-x root/root 0 2009-11-24 08:02 ./ drwxr-xr-x root/root 0 2009-11-24 08:02 ./usr/ drwxr-xr-x root/root 0 2009-11-24 08:03 ./usr/bin/ -rwxr-xr-x root/root 736180 2009-11-24 08:03 ./usr/bin/theseus -rwxr-xr-x root/root 6168 2009-11-24 07:57 ./usr/bin/theseus_align drwxr-xr-x root/root 0 2009-11-24 08:02 ./usr/share/ drwxr-xr-x root/root 0 2009-11-24 08:02 ./usr/share/doc/ drwxr-xr-x root/root 0 2009-11-24 08:03 ./usr/share/doc/theseus/ -rw-r--r-- root/root 1439 2009-11-24 07:56 ./usr/share/doc/theseus/changelog.Debian.gz -rw-r--r-- root/root 1483 2009-11-24 07:56 ./usr/share/doc/theseus/citation.bib drwxr-xr-x root/root 0 2009-11-24 08:03 ./usr/share/doc/theseus/examples/ -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1csu__.pdb.fst -rw-r--r-- root/root 17321 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1u74d_.pdb.gz -rw-r--r-- root/root 16205 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1lfma_.pdb.gz -rw-r--r-- root/root 18950 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1cih__.pdb.gz -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1cih__.pdb.fst -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1u74d_.pdb.fst -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1csx__.pdb.fst -rw-r--r-- root/root 19250 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1crj__.pdb.gz -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1yeb__.pdb.fst -rw-r--r-- root/root 19115 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1yeb__.pdb.gz -rw-r--r-- root/root 17493 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1kyow_.pdb.gz -rw-r--r-- root/root 1576 2009-11-24 07:56 ./usr/share/doc/theseus/examples/getexamples -rw-r--r-- root/root 18807 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d2pcbb_.pdb.gz -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1kyow_.pdb.fst -rw-r--r-- root/root 1642 2008-09-09 02:52 ./usr/share/doc/theseus/examples/cytc.aln -rw-r--r-- root/root 27825 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1m60a_.pdb.gz -rw-r--r-- root/root 180 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d2pcbb_.pdb.fst -rw-r--r-- root/root 200 2007-12-12 21:11 ./usr/share/doc/theseus/examples/cytc.filemap -rw-r--r-- root/root 572182 2006-10-20 15:56 ./usr/share/doc/theseus/examples/1s40.pdb.gz -rw-r--r-- root/root 184 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1crj__.pdb.fst -rw-r--r-- root/root 1349 2006-10-20 15:56 ./usr/share/doc/theseus/examples/README -rw-r--r-- root/root 180 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1m60a_.pdb.fst -rw-r--r-- root/root 19001 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1csx__.pdb.gz -rw-r--r-- root/root 19091 2006-10-20 15:56 ./usr/share/doc/theseus/examples/d1csu__.pdb.gz -rw-r--r-- root/root 179 2008-09-09 02:52 ./usr/share/doc/theseus/examples/d1lfma_.pdb.fst -rw-r--r-- root/root 3915 2009-11-24 07:56 ./usr/share/doc/theseus/copyright -rw-r--r-- root/root 468 2009-11-24 07:56 ./usr/share/doc/theseus/README.Debian drwxr-xr-x root/root 0 2009-11-24 08:02 ./usr/share/man/ drwxr-xr-x root/root 0 2009-11-24 08:03 ./usr/share/man/man1/ -rw-r--r-- root/root 1412 2009-11-24 08:02 ./usr/share/man/man1/theseus_align.1.gz -rw-r--r-- root/root 7783 2009-11-24 08:02 ./usr/share/man/man1/theseus.1.gz theseus_1.4.3-2_armel.changes: Format: 1.8 Date: Thu, 03 Sep 2009 08:49:22 +0200 Source: theseus Binary: theseus Architecture: armel Version: 1.4.3-2 Distribution: lucid Urgency: low Maintainer: Ubuntu/armel Build Daemon Changed-By: Andreas Tille Description: theseus - superimpose macromolecules using maximum likelihood Closes: 542879 Changes: theseus (1.4.3-2) unstable; urgency=low . * debian/patches/10_kbsd.patch: Correctly applied patch from Cyril (sorry for mixing this up) Closes: #542879 Checksums-Sha1: 2221415b1adcaaecb3ee5796ab9e84419177a7e7 1147110 theseus_1.4.3-2_armel.deb Checksums-Sha256: f0964685fa048186558c746a7737e4e67a82bf08c395255740d9a50dd2d4b020 1147110 theseus_1.4.3-2_armel.deb Files: e86bb3b4cb30ee4c23c742ccb6c22227 1147110 science optional theseus_1.4.3-2_armel.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/theseus-1.4.3 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge intltool-debian groff-base liblapack3gf libglib2.0-0 gettext file diffstat html2text gettext-base debhelper autotools-dev po-debconf quilt libcroco3 libmagic1 libblas3gf liblapack-dev libgfortran3 libgsl0-dev libxml2 bsdmainutils libgsl0ldbl libpcre3 libblas-dev man-db libtool (Reading database ... 11916 files and directories currently installed.) Removing debhelper ... Removing po-debconf ... Removing quilt ... Purging configuration files for quilt ... Removing liblapack-dev ... Removing libgsl0-dev ... Removing libgsl0ldbl ... Purging configuration files for libgsl0ldbl ... Removing libblas-dev ... Removing man-db ... Purging configuration files for man-db ... Removing libtool ... Removing intltool-debian ... Removing groff-base ... Purging configuration files for groff-base ... Removing liblapack3gf ... Purging configuration files for liblapack3gf ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing diffstat ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing autotools-dev ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libblas3gf ... Purging configuration files for libblas3gf ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing libglib2.0-0 ... Purging configuration files for libglib2.0-0 ... Removing libpcre3 ... Purging configuration files for libpcre3 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20091124-0803 Build needed 00:06:52, 19176k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '1362496-2822891'] Scanning for processes to kill in build /srv/home/buildd/build-1362496-2822891/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '1362496-2822891'] Unmounting chroot for build 1362496-2822891... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '1362496-2822891'] Removing build 1362496-2822891