sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ clonalframe 1.2-3 (armhf) 14 May 2012 02:04 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: clonalframe Version: 1.2-3 Source Version: 1.2-3 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/clonalframe-76OCy_/clonalframe-1.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/clonalframe-76OCy_' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-b00bdc30-3e8f-4d02-a7aa-4e2b9c629560' 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: 'clonalframe' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/clonalframe/trunk Need to get 51.2 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main clonalframe 1.2-3 (dsc) [1399 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main clonalframe 1.2-3 (tar) [45.5 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main clonalframe 1.2-3 (diff) [4317 B] Fetched 51.2 kB in 0s (1307 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-yuNKmt/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 14 not upgraded. Need to get 0 B/706 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 ... 10676 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), qt4-qmake, libgsl0-dev, libqt4-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), qt4-qmake, libgsl0-dev, libqt4-dev dpkg-deb: building package `sbuild-build-depends-clonalframe-dummy' in `/«BUILDDIR»/resolver-sQctzr/apt_archive/sbuild-build-depends-clonalframe-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install clonalframe build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file fontconfig fontconfig-config gettext gettext-base groff-base html2text intltool-debian libaudio2 libcroco3 libdbus-1-3 libexpat1 libffi5 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0-dev libgsl0ldbl libice6 libjbig0 libjpeg8 liblcms1 libmagic1 libmng1 libpcre3 libpipeline1 libpng12-0 libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-help libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtgui4 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 libxt6 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake ttf-dejavu-core x11-common Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff nas gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html liblcms-utils libqt4-declarative-folderlistmodel libqt4-declarative-gestures libqt4-declarative-particles libqt4-declarative-shaders qt4-qmlviewer firebird2.1-dev libmysqlclient-dev libpq-dev libsqlite0-dev libsqlite3-dev qt4-dev-tools qt4-doc unixodbc-dev qt4-qtconfig less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint dbus libglib2.0-data shared-mime-info libqt4-opengl-dev libqtwebkit-dev libqt4-sql-mysql libqt4-sql-odbc libqt4-sql-psql libqt4-sql-sqlite libqt4-sql-sqlite2 libcups2 xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file fontconfig fontconfig-config gettext gettext-base groff-base html2text intltool-debian libaudio2 libcroco3 libdbus-1-3 libexpat1 libffi5 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0-dev libgsl0ldbl libice6 libjbig0 libjpeg8 liblcms1 libmagic1 libmng1 libpcre3 libpipeline1 libpng12-0 libqt4-dbus libqt4-declarative libqt4-designer libqt4-dev libqt4-help libqt4-network libqt4-qt3support libqt4-script libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns libqtcore4 libqtgui4 libsm6 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 libxt6 man-db po-debconf qdbus qt4-linguist-tools qt4-qmake sbuild-build-depends-clonalframe-dummy ttf-dejavu-core x11-common debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 65 newly installed, 0 to remove and 14 not upgraded. Need to get 0 B/41.9 MB of archives. After this operation, 110 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10676 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 libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libxau6:armhf. Unpacking libxau6:armhf (from .../libxau6_1%3a1.0.7-1_armhf.deb) ... Selecting previously unselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.6+13_all.deb) ... Selecting previously unselected package libice6:armhf. 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Unpacking libqt4-svg (from .../libqt4-svg_4%3a4.7.4-3+rpi2_armhf.deb) ... Selecting previously unselected package libqt4-test. Unpacking libqt4-test (from .../libqt4-test_4%3a4.7.4-3+rpi2_armhf.deb) ... Selecting previously unselected package qt4-linguist-tools. Unpacking qt4-linguist-tools (from .../qt4-linguist-tools_4%3a4.7.4-3+rpi2_armhf.deb) ... Selecting previously unselected package qt4-qmake. Unpacking qt4-qmake (from .../qt4-qmake_4%3a4.7.4-3+rpi2_armhf.deb) ... Selecting previously unselected package libqt4-dev. Unpacking libqt4-dev (from .../libqt4-dev_4%3a4.7.4-3+rpi2_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-clonalframe-dummy. Unpacking sbuild-build-depends-clonalframe-dummy (from .../sbuild-build-depends-clonalframe-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up x11-common (1:7.6+13) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.8-2) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.99.901-2) ... Setting up libx11-6:armhf (2:1.4.99.901-2) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up libaudio2:armhf (1.9.3-5) ... 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 libdbus-1-3:armhf (1.5.12-1) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.9.0-3) ... Setting up libfontconfig1:armhf (2.9.0-3) ... Setting up libjpeg8:armhf (8d-1) ... Setting up liblcms1 (1.19.dfsg-1) ... Setting up libmng1:armhf (1.0.10-3) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libjbig0:armhf (2.0-2) ... Setting up libtiff4:armhf (3.9.6-5) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxrender1:armhf (1:0.9.7-1) ... 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 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 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 fontconfig (2.9.0-3) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libgsl0ldbl (1.15+dfsg-1) ... Setting up libgsl0-dev (1.15+dfsg-1) ... Setting up libqtcore4 (4:4.7.4-3+rpi2) ... Setting up libqt4-xml (4:4.7.4-3+rpi2) ... Setting up libqt4-sql (4:4.7.4-3+rpi2) ... Setting up libqtgui4 (4:4.7.4-3+rpi2) ... Setting up libqt4-svg (4:4.7.4-3+rpi2) ... Setting up libqt4-test (4:4.7.4-3+rpi2) ... Setting up qt4-linguist-tools (4:4.7.4-3+rpi2) ... update-alternatives: using /usr/bin/lupdate-qt4 to provide /usr/bin/lupdate (lupdate) in auto mode. update-alternatives: using /usr/bin/lrelease-qt4 to provide /usr/bin/lrelease (lrelease) in auto mode. Setting up qt4-qmake (4:4.7.4-3+rpi2) ... update-alternatives: using /usr/bin/qmake-qt4 to provide /usr/bin/qmake (qmake) in auto mode. Setting up qdbus (4:4.7.4-3+rpi2) ... Setting up libqt4-dbus (4:4.7.4-3+rpi2) ... Setting up libqt4-network (4:4.7.4-3+rpi2) ... Setting up libqt4-script (4:4.7.4-3+rpi2) ... Setting up libqt4-xmlpatterns (4:4.7.4-3+rpi2) ... Setting up libqt4-declarative (4:4.7.4-3+rpi2) ... Setting up libqt4-designer (4:4.7.4-3+rpi2) ... Setting up libqt4-help (4:4.7.4-3+rpi2) ... Setting up libqt4-qt3support (4:4.7.4-3+rpi2) ... Setting up libqt4-scripttools (4:4.7.4-3+rpi2) ... Setting up libqt4-dev (4:4.7.4-3+rpi2) ... update-alternatives: using /usr/bin/moc-qt4 to provide /usr/bin/moc (moc) in auto mode. update-alternatives: using /usr/bin/uic-qt4 to provide /usr/bin/uic (uic) in auto mode. update-alternatives: warning: skip creation of /usr/share/man/man1/uic.1.gz because associated file /usr/share/man/man1/uic-qt4.1.gz (of link group uic) doesn't exist. Setting up sbuild-build-depends-clonalframe-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_2.13-30 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: 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 fontconfig_2.9.0-3 fontconfig-config_2.9.0-3 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 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 libaudio2_1.9.3-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdbus-1-3_1.5.12-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfontconfig1_2.9.0-3 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libgsl0-dev_1.15+dfsg-1 libgsl0ldbl_1.15+dfsg-1 libice6_2:1.0.8-2 libjbig0_2.0-2 libjpeg8_8d-1 liblcms1_1.19.dfsg-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmng1_1.0.10-3 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 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 libpng12-0_1.2.49-1 libqt4-dbus_4:4.7.4-3+rpi2 libqt4-declarative_4:4.7.4-3+rpi2 libqt4-designer_4:4.7.4-3+rpi2 libqt4-dev_4:4.7.4-3+rpi2 libqt4-help_4:4.7.4-3+rpi2 libqt4-network_4:4.7.4-3+rpi2 libqt4-qt3support_4:4.7.4-3+rpi2 libqt4-script_4:4.7.4-3+rpi2 libqt4-scripttools_4:4.7.4-3+rpi2 libqt4-sql_4:4.7.4-3+rpi2 libqt4-svg_4:4.7.4-3+rpi2 libqt4-test_4:4.7.4-3+rpi2 libqt4-xml_4:4.7.4-3+rpi2 libqt4-xmlpatterns_4:4.7.4-3+rpi2 libqtcore4_4:4.7.4-3+rpi2 libqtgui4_4:4.7.4-3+rpi2 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 libsm6_2:1.2.1-2 libss2_1.42.2-2 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 libtiff4_3.9.6-5 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 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 libx11-6_2:1.4.99.901-2 libx11-data_2:1.4.99.901-2 libxau6_1:1.0.7-1 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.1-2 libxml2_2.7.8.dfsg-9 libxrender1_1:0.9.7-1 libxt6_1:1.1.3-1 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 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 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 qdbus_4:4.7.4-3+rpi2 qt4-linguist-tools_4:4.7.4-3+rpi2 qt4-qmake_4:4.7.4-3+rpi2 readline-common_6.2-8 sbuild-build-depends-clonalframe-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 ttf-dejavu-core_2.33-2 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 x11-common_1:7.6+13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Jan 7 08:32:26 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clonalframe_1.2-3.dsc dpkg-source: info: extracting clonalframe in clonalframe-1.2 dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz dpkg-source: info: unpacking clonalframe_1.2-3.debian.tar.gz dpkg-source: info: applying 01_gcc-4.6.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-b00bdc30-3e8f-4d02-a7aa-4e2b9c629560 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package clonalframe dpkg-buildpackage: source version 1.2-3 dpkg-source --before-build clonalframe-1.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_clean rm -rf bin build Makefile make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' qmake; /usr/bin/make make[2]: Entering directory `/«PKGBUILDDIR»' g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment_xmfa.o src/alignment_xmfa.cpp src/alignment_xmfa.cpp: In constructor 'wb::Alignment_xmfa::Alignment_xmfa(char*, bool, int)': src/alignment_xmfa.cpp:129:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment_structure.o src/alignment_structure.cpp src/alignment_structure.cpp: In constructor 'wb::Alignment_structure::Alignment_structure(char*, int)': src/alignment_structure.cpp:45:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/alignment.o src/alignment.cpp src/alignment.cpp: In member function 'void wb::Alignment::writeToFile(char*)': src/alignment.cpp:236:21: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] src/alignment.cpp:241:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/alignment.cpp:243:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/alignment.cpp:244:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/alignment.cpp:246:41: warning: embedded '\0' in format [-Wformat-contains-nul] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/boot.o src/boot.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/burst.o src/burst.cpp src/burst.cpp: In member function 'void wb::Burst::burst(wb::Param*)': src/burst.cpp:188:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/burst.cpp:190:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/burst.cpp: In member function 'void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector >*, int)': src/burst.cpp:259:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/burst.cpp: At global scope: src/burst.cpp:252:10: warning: unused parameter 'f' [-Wunused-parameter] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/consensus.o src/consensus.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/genes.o src/genes.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/hashcell.o src/hashcell.cpp src/hashcell.cpp: In member function 'void wb::HashCell::addNode(wb::Tree*)': src/hashcell.cpp:51:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_ages.o src/move_ages.cpp src/move_ages.cpp: In member function 'virtual void wb::Move_ages::move(wb::Param*)': src/move_ages.cpp:60:21: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_delta.o src/move_delta.cpp src/move_delta.cpp:24:5: warning: unused parameter 'p' [-Wunused-parameter] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_gap.o src/move_gap.cpp src/move_gap.cpp:24:5: warning: unused parameter 'p' [-Wunused-parameter] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_hidden.o src/move_hidden.cpp src/move_hidden.cpp:25:5: warning: unused parameter 'p' [-Wunused-parameter] src/move_hidden.cpp: In member function 'void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)': src/move_hidden.cpp:127:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/move_hidden.cpp:133:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/move_hidden.cpp:137:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/move_hidden.cpp:132:21: warning: unused variable 'top' [-Wunused-variable] src/move_hidden.cpp:132:27: warning: unused variable 'left' [-Wunused-variable] src/move_hidden.cpp:132:34: warning: unused variable 'right' [-Wunused-variable] src/move_hidden.cpp: In member function 'void wb::Move_hidden::backward(wb::Param*, gsl_matrix*, wb::Tree*)': src/move_hidden.cpp:203:17: warning: unused variable 'd' [-Wunused-variable] src/move_hidden.cpp: In member function 'void wb::Move_hidden::makee(wb::Param*, wb::Tree*)': src/move_hidden.cpp:410:66: warning: 'm1' may be used uninitialized in this function [-Wuninitialized] src/move_hidden.cpp: In member function 'int wb::Move_hidden::setState(wb::Tree*, wb::Param*, int, gsl_vector*)': src/move_hidden.cpp:271:64: warning: 'r' may be used uninitialized in this function [-Wuninitialized] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_hidden2.o src/move_hidden2.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_mu.o src/move_mu.cpp src/move_mu.cpp:24:5: warning: unused parameter 'p' [-Wunused-parameter] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_nu.o src/move_nu.cpp src/move_nu.cpp:24:5: warning: unused parameter 'p' [-Wunused-parameter] src/move_nu.cpp: In member function 'virtual void wb::Move_nu::move(wb::Param*)': src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_rho.o src/move_rho.cpp src/move_rho.cpp:24:5: warning: unused parameter 'p' [-Wunused-parameter] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move_wb.o src/move_wb.cpp src/move_wb.cpp: In member function 'virtual void wb::Move_wb::move(wb::Param*)': src/move_wb.cpp:127:17: warning: unused variable 'sizeys2' [-Wunused-variable] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/move.o src/move.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/param.o src/param.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/recorder.o src/recorder.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_coal.o src/tree_coal.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_simple.o src/tree_simple.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_upgma.o src/tree_upgma.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree_newick.o src/tree_newick.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/tree.o src/tree.cpp src/tree.cpp: In static member function 'static wb::Tree* wb::Tree::move(wb::Tree*, wb::Tree*, double, gsl_vector_char*, gsl_vector_char*, wb::Param*)': src/tree.cpp:99:12: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] src/tree.cpp: In member function 'double wb::Tree::llhoodb(wb::Param*)': src/tree.cpp:229:96: warning: 'vals[9]' may be used uninitialized in this function [-Wuninitialized] src/tree.cpp:223:38: warning: 'vals[5]' may be used uninitialized in this function [-Wuninitialized] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/util.o src/util.cpp src/util.cpp: In static member function 'static void wb::Util::normalize(double*, int)': src/util.cpp:83:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/util.cpp:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4 -Ibuild -o build/ClonalFrame.o src/ClonalFrame.cpp src/ClonalFrame.cpp: In function 'gsl_rng* makerng()': src/ClonalFrame.cpp:83:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable] src/ClonalFrame.cpp: In function 'int main(int, char**)': src/ClonalFrame.cpp:263:68: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] src/ClonalFrame.cpp:341:51: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat] g++ -Wl,-O1 -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -L/usr/lib -lgsl -lgslcblas -lQtGui -lQtCore -lpthread make[2]: Leaving directory `/«PKGBUILDDIR»' 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/clonalframe/usr/bin/ClonalFrame 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/clonalframe/usr/bin/ClonalFrame was not linked against libQtGui.so.4 (it uses none of the library's symbols). dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libQtCore.so.4 (it uses none of the library's symbols). dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clonalframe/usr/bin/ClonalFrame was not linked against libgslcblas.so.0 (it uses none of the library's symbols). dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `clonalframe' in `../clonalframe_1.2-3_armhf.deb'. dpkg-genchanges -B -mbuildd >../clonalframe_1.2-3_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 clonalframe-1.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120514-0209 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ clonalframe_1.2-3_armhf.changes: ──────────────────────────────── Format: 1.8 Date: Sat, 07 Jan 2012 09:26:15 +0100 Source: clonalframe Binary: clonalframe Architecture: armhf Version: 1.2-3 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: clonalframe - inference of bacterial microevolution using multilocus sequence d Closes: 650474 Changes: clonalframe (1.2-3) unstable; urgency=low . [ A. Costa ] * Corrected typos in debian/ClonalFrame.1 (Closes: #650474). . [ Andreas Tille ] * debian/control: - Fixed Vcs fields - Remove quilt from build-depends Checksums-Sha1: 5798516d097dd0d518d71c39c522632e5e9cd851 51194 clonalframe_1.2-3_armhf.deb Checksums-Sha256: bf0b628c903999cf14cef991bfe408ab16e24bb536dba69290b4d59f2b7eab71 51194 clonalframe_1.2-3_armhf.deb Files: d8f92806418c7165347d83f31cb1e71c 51194 science optional clonalframe_1.2-3_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ clonalframe_1.2-3_armhf.deb ─────────────────────────── new debian package, version 2.0. size 51194 bytes: control archive= 1024 bytes. 1259 bytes, 22 lines control 274 bytes, 4 lines md5sums Package: clonalframe Version: 1.2-3 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 128 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgsl0ldbl (>= 1.9), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0) Section: science Priority: optional Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Description: inference of bacterial microevolution using multilocus sequence data ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. . ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame. drwxr-xr-x root/root 0 2012-05-14 02:08 ./ drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/ drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/share/ drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/share/doc/clonalframe/ -rw-r--r-- root/root 424 2012-01-07 00:27 ./usr/share/doc/clonalframe/changelog.Debian.gz -rw-r--r-- root/root 1268 2011-12-06 23:37 ./usr/share/doc/clonalframe/copyright drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/share/man/man1/ -rw-r--r-- root/root 1055 2012-05-14 02:08 ./usr/share/man/man1/ClonalFrame.1.gz drwxr-xr-x root/root 0 2012-05-14 02:08 ./usr/bin/ -rwxr-xr-x root/root 90820 2012-05-14 02:08 ./usr/bin/ClonalFrame ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* file* fontconfig* fontconfig-config* gettext* gettext-base* groff-base* html2text* intltool-debian* libaudio2* libcroco3* libdbus-1-3* libexpat1* libffi5* libfontconfig1* libfreetype6* libglib2.0-0* libgsl0-dev* libgsl0ldbl* libice6* libjbig0* libjpeg8* liblcms1* libmagic1* libmng1* libpcre3* libpipeline1* libpng12-0* libqt4-dbus* libqt4-declarative* libqt4-designer* libqt4-dev* libqt4-help* libqt4-network* libqt4-qt3support* libqt4-script* libqt4-scripttools* libqt4-sql* libqt4-svg* libqt4-test* libqt4-xml* libqt4-xmlpatterns* libqtcore4* libqtgui4* libsm6* libtiff4* libunistring0* libx11-6* libx11-data* libxau6* libxcb1* libxdmcp6* libxext6* libxml2* libxrender1* libxt6* man-db* po-debconf* qdbus* qt4-linguist-tools* qt4-qmake* sbuild-build-depends-clonalframe-dummy* sbuild-build-depends-core-dummy* ttf-dejavu-core* x11-common* 0 upgraded, 0 newly installed, 66 to remove and 14 not upgraded. After this operation, 110 MB disk space will be freed. (Reading database ... 16519 files and directories currently installed.) Removing sbuild-build-depends-clonalframe-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing libqt4-dev ... Removing libqt4-svg ... Purging configuration files for libqt4-svg ... Removing libqt4-scripttools ... Purging configuration files for libqt4-scripttools ... Removing libqt4-qt3support ... Purging configuration files for libqt4-qt3support ... Removing libqt4-help ... Purging configuration files for libqt4-help ... Removing libqt4-designer ... Purging configuration files for libqt4-designer ... Removing libqt4-declarative ... Purging configuration files for libqt4-declarative ... Removing libqtgui4 ... Purging configuration files for libqtgui4 ... Removing fontconfig ... 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Purging configuration files for libpcre3:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 1068 Build-Time: 199 Distribution: testing Install-Time: 125 Job: clonalframe_1.2-3 Package: clonalframe Package-Time: 340 Source-Version: 1.2-3 Space: 1068 Status: successful Version: 1.2-3 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120514-0209 Build needed 00:05:40, 1068k disc space