sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ autodock-vina 1.1.2-2 (armhf) 14 May 2012 01:07 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: autodock-vina Version: 1.1.2-2 Source Version: 1.1.2-2 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/autodock-vina-_aI94Z/autodock-vina-1.1.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/autodock-vina-_aI94Z' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-360ebc96-21d4-4395-bb82-42dba2788c7b' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'autodock-vina' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/autodock-vina/trunk/ Need to get 76.3 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main autodock-vina 1.1.2-2 (dsc) [1493 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main autodock-vina 1.1.2-2 (tar) [69.5 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main autodock-vina 1.1.2-2 (diff) [5334 B] Fetched 76.3 kB in 0s (1900 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-iImcCH/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10675 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), libboost-all-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), libboost-all-dev dpkg-deb: building package `sbuild-build-depends-autodock-vina-dummy' in `/«BUILDDIR»/resolver-4xRJKU/apt_archive/sbuild-build-depends-autodock-vina-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install autodock-vina build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: adduser bsdmainutils debhelper file gccxml gettext gettext-base groff-base html2text intltool-debian libboost-all-dev libboost-chrono-dev libboost-chrono1.49-dev libboost-chrono1.49.0 libboost-date-time-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev libboost-filesystem-dev libboost-filesystem1.49-dev libboost-filesystem1.49.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.49-dev libboost-graph1.49-dev libboost-iostreams-dev libboost-iostreams1.49-dev libboost-iostreams1.49.0 libboost-locale-dev libboost-locale1.49-dev libboost-locale1.49.0 libboost-math-dev libboost-math1.49-dev libboost-math1.49.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.49-dev libboost-mpi-python1.49.0 libboost-mpi1.49-dev libboost-mpi1.49.0 libboost-program-options-dev libboost-program-options1.49-dev libboost-program-options1.49.0 libboost-python-dev libboost-python1.49-dev libboost-python1.49.0 libboost-random-dev libboost-random1.49-dev libboost-random1.49.0 libboost-regex-dev libboost-regex1.49-dev libboost-regex1.49.0 libboost-serialization-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-signals-dev libboost-signals1.49-dev libboost-signals1.49.0 libboost-system-dev libboost-system1.49-dev libboost-system1.49.0 libboost-test-dev libboost-test1.49-dev libboost-test1.49.0 libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0 libboost-timer-dev libboost-timer1.49-dev libboost-timer1.49.0 libboost-wave-dev libboost-wave1.49-dev libboost-wave1.49.0 libboost1.49-dev libcroco3 libexpat1 libexpat1-dev libffi5 libgfortran3 libglib2.0-0 libibverbs-dev libibverbs1 libicu-dev libicu48 libmagic1 libopenmpi-dev libopenmpi1.3 libpcre3 libpipeline1 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtorque2 libunistring0 libxml2 man-db mime-support mpi-default-dev openmpi-common po-debconf python python-dev python-minimal python2.7 python2.7-dev python2.7-minimal zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff libboost-doc python3 libboost1.49-doc xsltproc doxygen docbook-xml docbook-xsl default-jdk fop icu-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl wget lynx-cur autopoint libboost-graph-parallel1.49.0 libboost-graph1.49.0 libglib2.0-data shared-mime-info libssl-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: adduser bsdmainutils debhelper file gccxml gettext gettext-base groff-base html2text intltool-debian libboost-all-dev libboost-chrono-dev libboost-chrono1.49-dev libboost-chrono1.49.0 libboost-date-time-dev libboost-date-time1.49-dev libboost-date-time1.49.0 libboost-dev libboost-filesystem-dev libboost-filesystem1.49-dev libboost-filesystem1.49.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.49-dev libboost-graph1.49-dev libboost-iostreams-dev libboost-iostreams1.49-dev libboost-iostreams1.49.0 libboost-locale-dev libboost-locale1.49-dev libboost-locale1.49.0 libboost-math-dev libboost-math1.49-dev libboost-math1.49.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.49-dev libboost-mpi-python1.49.0 libboost-mpi1.49-dev libboost-mpi1.49.0 libboost-program-options-dev libboost-program-options1.49-dev libboost-program-options1.49.0 libboost-python-dev libboost-python1.49-dev libboost-python1.49.0 libboost-random-dev libboost-random1.49-dev libboost-random1.49.0 libboost-regex-dev libboost-regex1.49-dev libboost-regex1.49.0 libboost-serialization-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost-signals-dev libboost-signals1.49-dev libboost-signals1.49.0 libboost-system-dev libboost-system1.49-dev libboost-system1.49.0 libboost-test-dev libboost-test1.49-dev libboost-test1.49.0 libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0 libboost-timer-dev libboost-timer1.49-dev libboost-timer1.49.0 libboost-wave-dev libboost-wave1.49-dev libboost-wave1.49.0 libboost1.49-dev libcroco3 libexpat1 libexpat1-dev libffi5 libgfortran3 libglib2.0-0 libibverbs-dev libibverbs1 libicu-dev libicu48 libmagic1 libopenmpi-dev libopenmpi1.3 libpcre3 libpipeline1 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtorque2 libunistring0 libxml2 man-db mime-support mpi-default-dev openmpi-common po-debconf python python-dev python-minimal python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-autodock-vina-dummy zlib1g-dev debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 109 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/90.8 MB of archives. After this operation, 295 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10675 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1b-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libsqlite3-0:armhf. Unpacking libsqlite3-0:armhf (from .../libsqlite3-0_3.7.11-3_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... 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Selecting previously unselected package libboost-all-dev. Unpacking libboost-all-dev (from .../libboost-all-dev_1.49.0.1_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-autodock-vina-dummy. Unpacking sbuild-build-depends-autodock-vina-dummy (from .../sbuild-build-depends-autodock-vina-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libssl1.0.0:armhf (1.0.1b-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libsqlite3-0:armhf (3.7.11-3) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libgfortran3:armhf (4.7.0-1.1+rpi) ... Setting up libicu48:armhf (4.8.1.1-6) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up adduser (3.113+nmu1) ... Setting up bsdmainutils (9.0.1) ... 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 groff-base (1.21-7) ... Setting up libboost-iostreams1.49.0 (1.49.0-2) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.3~rc2-2.1) ... Setting up python2.7 (2.7.3~rc2-2.1) ... Setting up python-minimal (2.7.2-10) ... Setting up python (2.7.2-10) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up gccxml (0.9.0+cvs20120420-2) ... 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Setting up libopenmpi-dev (1.4.3-2.1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode. Setting up mpi-default-dev (1.0.1) ... Setting up libboost-mpi1.49-dev (1.49.0-2) ... Setting up libboost-mpi-dev (1.49.0.1) ... Setting up libboost-python1.49.0 (1.49.0-2) ... Setting up libboost-mpi-python1.49.0 (1.49.0-2) ... Setting up libboost-mpi-python1.49-dev (1.49.0-2) ... Setting up libboost-mpi-python-dev (1.49.0.1) ... Setting up libboost-program-options1.49.0 (1.49.0-2) ... Setting up libboost-program-options1.49-dev (1.49.0-2) ... Setting up libboost-program-options-dev (1.49.0.1) ... Setting up libpython2.7 (2.7.3~rc2-2.1) ... Setting up libexpat1-dev (2.1.0-1) ... Setting up zlib1g-dev:armhf (1:1.2.6.dfsg-2) ... Setting up libssl-dev (1.0.1b-1) ... Setting up python2.7-dev (2.7.3~rc2-2.1) ... Setting up python-dev (2.7.2-10) ... Setting up libboost-python1.49-dev (1.49.0-2) ... Setting up libboost-python-dev (1.49.0.1) ... 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Setting up sbuild-build-depends-autodock-vina-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: adduser_3.113+nmu1 apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gccxml_0.9.0+cvs20120420-2 gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libboost-all-dev_1.49.0.1 libboost-chrono-dev_1.49.0.1 libboost-chrono1.49-dev_1.49.0-2 libboost-chrono1.49.0_1.49.0-2 libboost-date-time-dev_1.49.0.1 libboost-date-time1.49-dev_1.49.0-2 libboost-date-time1.49.0_1.49.0-2 libboost-dev_1.49.0.1 libboost-filesystem-dev_1.49.0.1 libboost-filesystem1.49-dev_1.49.0-2 libboost-filesystem1.49.0_1.49.0-2 libboost-graph-dev_1.49.0.1 libboost-graph-parallel-dev_1.49.0.1 libboost-graph-parallel1.49-dev_1.49.0-2 libboost-graph1.49-dev_1.49.0-2 libboost-iostreams-dev_1.49.0.1 libboost-iostreams1.49-dev_1.49.0-2 libboost-iostreams1.49.0_1.49.0-2 libboost-locale-dev_1.49.0.1 libboost-locale1.49-dev_1.49.0-2 libboost-locale1.49.0_1.49.0-2 libboost-math-dev_1.49.0.1 libboost-math1.49-dev_1.49.0-2 libboost-math1.49.0_1.49.0-2 libboost-mpi-dev_1.49.0.1 libboost-mpi-python-dev_1.49.0.1 libboost-mpi-python1.49-dev_1.49.0-2 libboost-mpi-python1.49.0_1.49.0-2 libboost-mpi1.49-dev_1.49.0-2 libboost-mpi1.49.0_1.49.0-2 libboost-program-options-dev_1.49.0.1 libboost-program-options1.49-dev_1.49.0-2 libboost-program-options1.49.0_1.49.0-2 libboost-python-dev_1.49.0.1 libboost-python1.49-dev_1.49.0-2 libboost-python1.49.0_1.49.0-2 libboost-random-dev_1.49.0.1 libboost-random1.49-dev_1.49.0-2 libboost-random1.49.0_1.49.0-2 libboost-regex-dev_1.49.0.1 libboost-regex1.49-dev_1.49.0-2 libboost-regex1.49.0_1.49.0-2 libboost-serialization-dev_1.49.0.1 libboost-serialization1.49-dev_1.49.0-2 libboost-serialization1.49.0_1.49.0-2 libboost-signals-dev_1.49.0.1 libboost-signals1.49-dev_1.49.0-2 libboost-signals1.49.0_1.49.0-2 libboost-system-dev_1.49.0.1 libboost-system1.49-dev_1.49.0-2 libboost-system1.49.0_1.49.0-2 libboost-test-dev_1.49.0.1 libboost-test1.49-dev_1.49.0-2 libboost-test1.49.0_1.49.0-2 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-2 libboost-thread1.49.0_1.49.0-2 libboost-timer-dev_1.49.0.1 libboost-timer1.49-dev_1.49.0-2 libboost-timer1.49.0_1.49.0-2 libboost-wave-dev_1.49.0.1 libboost-wave1.49-dev_1.49.0-2 libboost-wave1.49.0_1.49.0-2 libboost1.49-dev_1.49.0-2 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libgfortran3_4.7.0-1.1+rpi libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libibverbs-dev_1.1.6-1 libibverbs1_1.1.6-1 libicu-dev_4.8.1.1-6 libicu48_4.8.1.1-6 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libopenmpi-dev_1.4.3-2.1 libopenmpi1.3_1.4.3-2.1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 libpython2.7_2.7.3~rc2-2.1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-10 libsqlite3-0_3.7.11-3 libss2_1.42.2-2 libssl-dev_1.0.1b-1 libssl1.0.0_1.0.1b-1 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 libtorque2_2.4.16+dfsg-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-4 mpi-default-dev_1.0.1 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 openmpi-common_1.4.3-2.1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-dev_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc2-2.1 python2.7-dev_2.7.3~rc2-2.1 python2.7-minimal_2.7.3~rc2-2.1 readline-common_6.2-8 sbuild-build-depends-autodock-vina-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Mon Nov 28 11:29:10 2011 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./autodock-vina_1.1.2-2.dsc dpkg-source: info: extracting autodock-vina in autodock-vina-1.1.2 dpkg-source: info: unpacking autodock-vina_1.1.2.orig.tar.gz dpkg-source: info: unpacking autodock-vina_1.1.2-2.debian.tar.gz dpkg-source: info: applying remove_static.patch dpkg-source: info: applying top_level_Makefile.patch dpkg-source: info: applying do_not_link_against_unneeded_libs.patch dpkg-source: info: applying annoying_static_removed_was_in_for_a_reason_questionmark.patch dpkg-source: info: applying fix_boost.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-360ebc96-21d4-4395-bb82-42dba2788c7b SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package autodock-vina dpkg-buildpackage: source version 1.1.2-2 dpkg-source --before-build autodock-vina-1.1.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh_clean rm -f build/linux/release/*.o build/linux/release/vina* debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' make BASE=/usr -C build/linux/release make[2]: Entering directory `/«PKGBUILDDIR»/build/linux/release' g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp /tmp/ccyISzi5.s: Assembler messages: /tmp/ccyISzi5.s:10085: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10095: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10112: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10171: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10181: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10198: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10309: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10319: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10336: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10408: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10418: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10435: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10914: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10923: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:10940: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:11002: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:11011: Warning: swp{b} use is deprecated for this architecture /tmp/ccyISzi5.s:11028: Warning: swp{b} use is deprecated for this architecture g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o cache.o -c ../../../src/lib/cache.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o coords.o -c ../../../src/lib/coords.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o current_weights.o -c ../../../src/lib/current_weights.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o everything.o -c ../../../src/lib/everything.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o grid.o -c ../../../src/lib/grid.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o szv_grid.o -c ../../../src/lib/szv_grid.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o manifold.o -c ../../../src/lib/manifold.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o model.o -c ../../../src/lib/model.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o monte_carlo.o -c ../../../src/lib/monte_carlo.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o mutate.o -c ../../../src/lib/mutate.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o my_pid.o -c ../../../src/lib/my_pid.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o naive_non_cache.o -c ../../../src/lib/naive_non_cache.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o non_cache.o -c ../../../src/lib/non_cache.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o parallel_mc.o -c ../../../src/lib/parallel_mc.cpp /tmp/cctk97Qy.s: Assembler messages: /tmp/cctk97Qy.s:2501: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2511: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2528: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2598: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2607: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2624: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2669: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2678: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:2695: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9295: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9304: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9321: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9689: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9698: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9715: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9753: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9762: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9779: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9813: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9823: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9841: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9878: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9887: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9904: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9939: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9948: Warning: swp{b} use is deprecated for this architecture /tmp/cctk97Qy.s:9965: Warning: swp{b} use is deprecated for this architecture g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o parse_pdbqt.o -c ../../../src/lib/parse_pdbqt.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o pdb.o -c ../../../src/lib/pdb.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o quasi_newton.o -c ../../../src/lib/quasi_newton.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o quaternion.o -c ../../../src/lib/quaternion.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o random.o -c ../../../src/lib/random.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o ssd.o -c ../../../src/lib/ssd.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o terms.o -c ../../../src/lib/terms.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -o weighted_terms.o -c ../../../src/lib/weighted_terms.cpp g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -L/usr/lib -L. -o vina main.o cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o -l boost_system -l boost_thread -l boost_program_options -lboost_filesystem g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -I ../../../src/lib -o split.o -c ../../../src/split/split.cpp /tmp/cc1bzGyw.s: Assembler messages: /tmp/cc1bzGyw.s:6988: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:6998: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7015: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7074: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7084: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7101: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7210: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7220: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7237: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7301: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7311: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7328: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7401: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7411: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7428: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7478: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7488: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7505: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7760: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7769: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7786: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7852: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7861: Warning: swp{b} use is deprecated for this architecture /tmp/cc1bzGyw.s:7878: Warning: swp{b} use is deprecated for this architecture g++ -pthread -ansi -Wno-long-long -O3 -DNDEBUG -I /usr/include -L/usr/lib -L. -o vina_split split.o -l boost_system -l boost_thread -l boost_program_options -lboost_filesystem make[2]: Leaving directory `/«PKGBUILDDIR»/build/linux/release' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a 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_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 dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/autodock-vina/usr/bin/vina contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/autodock-vina/usr/bin/vina_split debian/autodock-vina/usr/bin/vina were not linked against libboost_filesystem.so.1.49.0 (they use none of the library's symbols). dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `autodock-vina' in `../autodock-vina_1.1.2-2_armhf.deb'. dpkg-genchanges -B -mbuildd >../autodock-vina_1.1.2-2_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build autodock-vina-1.1.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120514-0125 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ autodock-vina_1.1.2-2_armhf.changes: ──────────────────────────────────── Format: 1.8 Date: Mon, 28 Nov 2011 10:58:42 +0100 Source: autodock-vina Binary: autodock-vina Architecture: armhf Version: 1.1.2-2 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: autodock-vina - docking of small molecules to proteins Closes: 642697 Changes: autodock-vina (1.1.2-2) unstable; urgency=low . * Fix boost compatibility error (thanks for the patch to Sebastian Ramacher ) Closes: #642697 * debian/control: Fixed Vcs fields * Debhelper 8 (control+compat) Checksums-Sha1: e451a8f4b1be4fd3d7fa81ae0a7a88e0e58ab2bd 277664 autodock-vina_1.1.2-2_armhf.deb Checksums-Sha256: 99ddc8531ffdba424192182cf3f93b4c531c3e497bac9735dfc71e76240ccf0d 277664 autodock-vina_1.1.2-2_armhf.deb Files: a2711348c93b5c99e3b184bcb3198f20 277664 science extra autodock-vina_1.1.2-2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ autodock-vina_1.1.2-2_armhf.deb ─────────────────────────────── new debian package, version 2.0. size 277664 bytes: control archive= 960 bytes. 1038 bytes, 21 lines control 386 bytes, 6 lines md5sums Package: autodock-vina Version: 1.1.2-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 638 Depends: libboost-filesystem1.49.0 (>= 1.49.0-1), libboost-program-options1.49.0 (>= 1.49.0-1), libboost-system1.49.0 (>= 1.49.0-1), libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6) Suggests: autodock, autogrid Section: science Priority: extra Homepage: http://vina.scripps.edu Description: docking of small molecules to proteins AutoDock Vina is a program to support drug discovery, molecular docking and virtual screening of compound libraries. It offers multi-core capability, high performance and enhanced accuracy and ease of use. . The same institute also developed autodock, which is widely used. . O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 drwxr-xr-x root/root 0 2012-05-14 01:24 ./ drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/ drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/share/ drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/share/man/man1/ -rw-r--r-- root/root 345 2012-05-14 01:24 ./usr/share/man/man1/vina_split.1.gz -rw-r--r-- root/root 774 2012-05-14 01:24 ./usr/share/man/man1/vina.1.gz drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/share/doc/autodock-vina/ -rw-r--r-- root/root 886 2011-11-28 03:27 ./usr/share/doc/autodock-vina/changelog.Debian.gz -rw-r--r-- root/root 1104 2010-11-13 11:12 ./usr/share/doc/autodock-vina/copyright drwxr-xr-x root/root 0 2012-05-14 01:24 ./usr/bin/ -rwxr-xr-x root/root 65688 2012-05-14 01:24 ./usr/bin/vina_split -rwxr-xr-x root/root 547452 2012-05-14 01:24 ./usr/bin/vina ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser* bsdmainutils* debhelper* file* gccxml* gettext* gettext-base* groff-base* html2text* intltool-debian* libboost-all-dev* libboost-chrono-dev* libboost-chrono1.49-dev* libboost-chrono1.49.0* libboost-date-time-dev* libboost-date-time1.49-dev* libboost-date-time1.49.0* libboost-dev* libboost-filesystem-dev* libboost-filesystem1.49-dev* libboost-filesystem1.49.0* libboost-graph-dev* libboost-graph-parallel-dev* libboost-graph-parallel1.49-dev* libboost-graph1.49-dev* libboost-iostreams-dev* libboost-iostreams1.49-dev* libboost-iostreams1.49.0* libboost-locale-dev* libboost-locale1.49-dev* libboost-locale1.49.0* libboost-math-dev* libboost-math1.49-dev* libboost-math1.49.0* libboost-mpi-dev* libboost-mpi-python-dev* libboost-mpi-python1.49-dev* libboost-mpi-python1.49.0* libboost-mpi1.49-dev* libboost-mpi1.49.0* libboost-program-options-dev* libboost-program-options1.49-dev* libboost-program-options1.49.0* libboost-python-dev* libboost-python1.49-dev* libboost-python1.49.0* libboost-random-dev* libboost-random1.49-dev* libboost-random1.49.0* libboost-regex-dev* libboost-regex1.49-dev* libboost-regex1.49.0* libboost-serialization-dev* libboost-serialization1.49-dev* libboost-serialization1.49.0* libboost-signals-dev* libboost-signals1.49-dev* libboost-signals1.49.0* libboost-system-dev* libboost-system1.49-dev* libboost-system1.49.0* libboost-test-dev* libboost-test1.49-dev* libboost-test1.49.0* libboost-thread-dev* libboost-thread1.49-dev* libboost-thread1.49.0* libboost-timer-dev* libboost-timer1.49-dev* libboost-timer1.49.0* libboost-wave-dev* libboost-wave1.49-dev* libboost-wave1.49.0* libboost1.49-dev* libcroco3* libexpat1* libexpat1-dev* libffi5* libgfortran3* libglib2.0-0* libibverbs-dev* libibverbs1* libicu-dev* libicu48* libmagic1* libopenmpi-dev* libopenmpi1.3* libpcre3* libpipeline1* libpython2.7* libsqlite3-0* libssl-dev* libssl1.0.0* libtorque2* libunistring0* libxml2* man-db* mime-support* mpi-default-dev* openmpi-common* po-debconf* python* python-dev* python-minimal* python2.7* python2.7-dev* python2.7-minimal* sbuild-build-depends-autodock-vina-dummy* sbuild-build-depends-core-dummy* zlib1g-dev* 0 upgraded, 0 newly installed, 110 to remove and 10 not upgraded. After this operation, 295 MB disk space will be freed. (Reading database ... 25416 files and directories currently installed.) Removing sbuild-build-depends-autodock-vina-dummy ... Removing libboost-all-dev ... Removing libboost-mpi-python-dev ... Removing libboost-mpi-python1.49-dev ... Removing libboost-mpi-dev ... Removing libboost-mpi1.49-dev ... Removing mpi-default-dev ... Removing libopenmpi-dev ... Removing libboost-mpi-python1.49.0 ... Purging configuration files for libboost-mpi-python1.49.0 ... Removing libboost-mpi1.49.0 ... Purging configuration files for libboost-mpi1.49.0 ... Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libibverbs-dev ... Removing libibverbs1 ... Purging configuration files for libibverbs1 ... Removing adduser ... Purging configuration files for adduser ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... 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Purging configuration files for libxml2:armhf ... Removing mime-support ... Purging configuration files for mime-support ... Removing openmpi-common ... Removing sbuild-build-depends-core-dummy ... Removing zlib1g-dev:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 4108 Build-Time: 829 Distribution: testing Install-Time: 221 Job: autodock-vina_1.1.2-2 Package: autodock-vina Package-Time: 1068 Source-Version: 1.1.2-2 Space: 4108 Status: successful Version: 1.1.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120514-0125 Build needed 00:17:48, 4108k disc space