sbuild (Debian sbuild) 0.63.1 (31 May 2012) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ r-bioc-biobase 2.14.0-1 (armhf) 14 Aug 2012 09:37 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: r-bioc-biobase Version: 2.14.0-1 Source Version: 2.14.0-1 Distribution: wheezy-staging Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf W: line 7 [wheezy-staging-armhf-sbuild]: Deprecated key ‘script-config’ used I: This option will be removed in the future; please update your configuration W: line 7 [testing-armhf-sbuild]: Deprecated key ‘script-config’ used I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-Yyqa1A/r-bioc-biobase-2.14.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-Yyqa1A' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/wheezy-staging-armhf-sbuild-231e6088-ef57-44a5-88e4-fff3e89e36c7' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://archive.raspbian.lan wheezy-staging InRelease Hit http://archive.raspbian.lan wheezy-staging/main Sources Hit http://archive.raspbian.lan wheezy-staging/main armhf Packages Ign http://archive.raspbian.lan wheezy-staging/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: 'r-bioc-biobase' packaging is maintained in the 'Git' version control system at: git://git.debian.org/git/debian-med/r-bioc-biobase.git Need to get 1934 kB of source archives. Get:1 http://archive.raspbian.lan/raspbian/ wheezy-staging/main r-bioc-biobase 2.14.0-1 (dsc) [2004 B] Get:2 http://archive.raspbian.lan/raspbian/ wheezy-staging/main r-bioc-biobase 2.14.0-1 (tar) [1926 kB] Get:3 http://archive.raspbian.lan/raspbian/ wheezy-staging/main r-bioc-biobase 2.14.0-1 (diff) [5645 B] Fetched 1934 kB in 0s (3420 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-yQxgyp/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 6 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 ... 10701 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), cdbs, debhelper (>= 8), r-base-dev (>= 2.10) Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), r-base-dev (>= 2.10) dpkg-deb: building package `sbuild-build-depends-r-bioc-biobase-dummy' in `/«BUILDDIR»/resolver-9xAIRh/apt_archive/sbuild-build-depends-r-bioc-biobase-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install r-bioc-biobase 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 cdbs debhelper file fontconfig fontconfig-config gettext gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgettextpo0 libgfortran3 libglib2.0-0 libice6 libjbig0 libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libmagic1 libncurses5-dev libpango1.0-0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libreadline-dev libreadline6-dev libsm6 libthai-data libthai0 libtiff4 libtinfo-dev libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf r-base-core r-base-dev tcl8.5 tk8.5 ttf-dejavu-core unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc gfortran-doc gfortran-4.6-doc libgfortran3-dbg groff ncurses-doc ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp less www-browser libmail-box-perl r-doc-info r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo texi2html tcl-tclreadline gvfs-bin Recommended packages: autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl r-recommended r-doc-html xterm x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bsdmainutils cdbs debhelper file fontconfig fontconfig-config gettext gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgettextpo0 libgfortran3 libglib2.0-0 libice6 libjbig0 libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libmagic1 libncurses5-dev libpango1.0-0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libreadline-dev libreadline6-dev libsm6 libthai-data libthai0 libtiff4 libtinfo-dev libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf r-base-core r-base-dev sbuild-build-depends-r-bioc-biobase-dummy tcl8.5 tk8.5 ttf-dejavu-core unzip x11-common xdg-utils zip zlib1g-dev debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 79 newly installed, 0 to remove and 6 not upgraded. Need to get 0 B/55.2 MB of archives. After this operation, 112 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10701 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libasprintf0c2:armhf. Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-2_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-5_armhf.deb) ... Selecting previously unselected package libexpat1:armhf. Unpacking libexpat1:armhf (from .../libexpat1_2.1.0-1_armhf.deb) ... 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Unpacking x11-common (from .../x11-common_1%3a7.7+1_all.deb) ... Selecting previously unselected package libice6:armhf. Unpacking libice6:armhf (from .../libice6_2%3a1.0.8-2_armhf.deb) ... Selecting previously unselected package libjpeg8:armhf. Unpacking libjpeg8:armhf (from .../libjpeg8_8d-1_armhf.deb) ... Selecting previously unselected package libthai-data. Unpacking libthai-data (from .../libthai-data_0.1.18-1_all.deb) ... Selecting previously unselected package libthai0:armhf. Unpacking libthai0:armhf (from .../libthai0_0.1.18-1_armhf.deb) ... Selecting previously unselected package libxft2:armhf. Unpacking libxft2:armhf (from .../libxft2_2.3.1-1_armhf.deb) ... Selecting previously unselected package fontconfig. Unpacking fontconfig (from .../fontconfig_2.9.0-7_armhf.deb) ... Selecting previously unselected package libpango1.0-0:armhf. Unpacking libpango1.0-0:armhf (from .../libpango1.0-0_1.30.0-1_armhf.deb) ... Selecting previously unselected package libpaper1:armhf. Unpacking libpaper1:armhf (from .../libpaper1_1.1.24+nmu2_armhf.deb) ... Selecting previously unselected package libpcrecpp0:armhf. Unpacking libpcrecpp0:armhf (from .../libpcrecpp0_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libsm6:armhf. Unpacking libsm6:armhf (from .../libsm6_2%3a1.2.1-2_armhf.deb) ... Selecting previously unselected package libjbig0:armhf. Unpacking libjbig0:armhf (from .../libjbig0_2.0-2_armhf.deb) ... Selecting previously unselected package libtiff4:armhf. Unpacking libtiff4:armhf (from .../libtiff4_3.9.6-7_armhf.deb) ... Selecting previously unselected package libxext6:armhf. Unpacking libxext6:armhf (from .../libxext6_2%3a1.3.1-2_armhf.deb) ... Selecting previously unselected package libxss1:armhf. Unpacking libxss1:armhf (from .../libxss1_1%3a1.2.2-1_armhf.deb) ... Selecting previously unselected package libxt6:armhf. Unpacking libxt6:armhf (from .../libxt6_1%3a1.1.3-1_armhf.deb) ... Selecting previously unselected package bsdmainutils. 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Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.1-5_armhf.deb) ... Selecting previously unselected package liblapack-dev. Unpacking liblapack-dev (from .../liblapack-dev_3.4.1-5_armhf.deb) ... Selecting previously unselected package libtinfo-dev:armhf. Unpacking libtinfo-dev:armhf (from .../libtinfo-dev_5.9-10_armhf.deb) ... Selecting previously unselected package libncurses5-dev. Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armhf.deb) ... Selecting previously unselected package libpaper-utils. Unpacking libpaper-utils (from .../libpaper-utils_1.1.24+nmu2_armhf.deb) ... Selecting previously unselected package libpcre3-dev. Unpacking libpcre3-dev (from .../libpcre3-dev_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package zlib1g-dev:armhf. Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armhf.deb) ... Selecting previously unselected package libpng12-dev. 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Unpacking r-base-core (from .../r-base-core_2.15.1-4_armhf.deb) ... Selecting previously unselected package r-base-dev. Unpacking r-base-dev (from .../r-base-dev_2.15.1-4_all.deb) ... Selecting previously unselected package sbuild-build-depends-r-bioc-biobase-dummy. Unpacking sbuild-build-depends-r-bioc-biobase-dummy (from .../sbuild-build-depends-r-bioc-biobase-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libasprintf0c2:armhf (0.18.1.1-9) ... Setting up libmagic1:armhf (5.11-2) ... Setting up libxml2:armhf (2.8.0+dfsg1-5) ... 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 (2.9.0-7) ... Setting up libfontconfig1:armhf (2.9.0-7) ... Setting up libpixman-1-0:armhf (0.26.0-3) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.5.0-1) ... Setting up libx11-6:armhf (2:1.5.0-1) ... Setting up libxcb-render0:armhf (1.8.1-1) ... Setting up libxcb-shm0:armhf (1.8.1-1) ... Setting up libxrender1:armhf (1:0.9.7-1) ... Setting up libcairo2:armhf (1.12.2-2) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libdatrie1:armhf (0.2.5-3) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libgettextpo0:armhf (0.18.1.1-9) ... Setting up libgfortran3:armhf (4.7.1-2+rpi1) ... Setting up x11-common (1:7.7+1) ... 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 libjpeg8:armhf (8d-1) ... Setting up libthai-data (0.1.18-1) ... Setting up libthai0:armhf (0.1.18-1) ... Setting up libxft2:armhf (2.3.1-1) ... Setting up fontconfig (2.9.0-7) ... Regenerating fonts cache... done. Setting up libpango1.0-0:armhf (1.30.0-1) ... Setting up libpaper1:armhf (1.1.24+nmu2) ... Creating config file /etc/papersize with new version Setting up libpcrecpp0:armhf (1:8.30-5) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libjbig0:armhf (2.0-2) ... Setting up libtiff4:armhf (3.9.6-7) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxss1:armhf (1:1.2.2-1) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up bsdmainutils (9.0.3) ... 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 (1.21-9) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-2) ... Setting up gettext-base (0.18.1.1-9) ... Setting up cdbs (0.4.115) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up gfortran-4.6 (4.6.3-8+rpi1) ... Setting up gfortran (4:4.6.3-7) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode. Setting up libblas-dev (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode. Setting up libbz2-dev:armhf (1.0.6-3) ... Setting up libjpeg8-dev:armhf (8d-1) ... Setting up liblapack3 (3.4.1-5) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode. Setting up liblapack-dev (3.4.1-5) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode. Setting up libtinfo-dev:armhf (5.9-10) ... Setting up libncurses5-dev (5.9-10) ... Setting up libpaper-utils (1.1.24+nmu2) ... Setting up libpcre3-dev (1:8.30-5) ... Setting up zlib1g-dev:armhf (1:1.2.7.dfsg-13) ... Setting up libpng12-dev (1.2.49-1) ... Setting up libreadline6-dev:armhf (6.2-8) ... Setting up libreadline-dev:armhf (6.2-8) ... Setting up zip (3.0-6) ... Setting up unzip (6.0-7) ... Setting up xdg-utils (1.1.0~rc1+git20111210-6) ... Setting up tcl8.5 (8.5.11-2) ... update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tk8.5 (8.5.11-2) ... update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode. Setting up r-base-core (2.15.1-4) ... Setting R_PAPERSIZE_USER default to 'a4' Creating config file /etc/R/Renviron with new version Setting up r-base-dev (2.15.1-4) ... Setting up sbuild-build-depends-r-bioc-biobase-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-8+rpi1 gcc-4.6_4.6.3-8+rpi1 libc6-dev_2.13-33 libstdc++6_4.7.1-2+rpi1 libstdc++6-4.6-dev_4.6.3-8+rpi1 linux-libc-dev_3.2.21-1+rpi1 Package versions: apt_0.9.3+rpi1 base-files_6.9 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.115 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8+rpi1 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debianutils_4.3.2 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 fontconfig_2.9.0-7 fontconfig-config_2.9.0-7 g++_4:4.6.3-7 g++-4.6_4.6.3-8+rpi1 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-8+rpi1 gcc-4.6-base_4.6.3-8+rpi1 gcc-4.7-base_4.7.1-2+rpi1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gfortran_4:4.6.3-7 gfortran-4.6_4.6.3-8+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 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_2.2.51-8 libapt-pkg4.12_0.9.3+rpi1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblas-dev_1.2.20110419-5 libblas3_1.2.20110419-5 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libbz2-dev_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libcairo2_1.12.2-2 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdatrie1_0.2.5-3 libdb5.1_5.1.29-5 libdpkg-perl_1.16.4.3 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfontconfig1_2.9.0-7 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2+rpi1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libgfortran3_4.7.1-2+rpi1 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-2+rpi1 libice6_2:1.0.8-2 libjbig0_2.0-2 libjpeg8_8d-1 libjpeg8-dev_8d-1 liblapack-dev_3.4.1-5 liblapack3_3.4.1-5 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpango1.0-0_1.30.0-1 libpaper-utils_1.1.24+nmu2 libpaper1_1.1.24+nmu2 libpcre3_1:8.30-5 libpcre3-dev_1:8.30-5 libpcrecpp0_1:8.30-5 libpipeline1_1.2.1-1 libpixman-1-0_0.26.0-3 libpng12-0_1.2.49-1 libpng12-dev_1.2.49-1 libreadline-dev_6.2-8 libreadline6_6.2-8 libreadline6-dev_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsm6_2:1.2.1-2 libss2_1.42.4-3 libstdc++6_4.7.1-2+rpi1 libstdc++6-4.6-dev_4.6.3-8+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.18-1 libthai0_0.1.18-1 libtiff4_3.9.6-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxau6_1:1.0.7-1 libxcb-render0_1.8.1-1 libxcb-shm0_1.8.1-1 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.1-2 libxft2_2.3.1-1 libxml2_2.8.0+dfsg1-5 libxrender1_1:0.9.7-1 libxss1_1:1.2.2-1 libxt6_1:1.1.3-1 linux-libc-dev_3.2.21-1+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12+rpi1 perl-base_5.14.2-12+rpi1 perl-modules_5.14.2-12+rpi1 po-debconf_1.0.16+nmu2 r-base-core_2.15.1-4 r-base-dev_2.15.1-4 raspbian-archive-keyring_20120528.2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-biobase-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tcl8.5_8.5.11-2 tk8.5_8.5.11-2 ttf-dejavu-core_2.33-2 tzdata_2012c-1 ucf_3.0025+nmu3 unzip_6.0-7 util-linux_2.20.1-5.1 x11-common_1:7.7+1 xdg-utils_1.1.0~rc1+git20111210-6 xz-utils_5.1.1alpha+20120614-1 zip_3.0-6 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed Nov 2 05:31:37 2011 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./r-bioc-biobase_2.14.0-1.dsc dpkg-source: info: extracting r-bioc-biobase in r-bioc-biobase-2.14.0 dpkg-source: info: unpacking r-bioc-biobase_2.14.0.orig.tar.gz dpkg-source: info: applying r-bioc-biobase_2.14.0-1.diff.gz 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_ALIAS_NAME=chroot:wheezy-staging-armhf-sbuild SCHROOT_CHROOT_NAME=wheezy-staging-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=wheezy-staging-armhf-sbuild-231e6088-ef57-44a5-88e4-fff3e89e36c7 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package r-bioc-biobase dpkg-buildpackage: source version 2.14.0-1 dpkg-source --before-build r-bioc-biobase-2.14.0 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules dh_testroot /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ "reverse-patches" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: if [ "reverse-patches" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "reverse-patches" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi for dir in debian/patches ; do \ rm -f $dir/*.log ; \ done dh_clean if test -d src; then \ find src -regex ".*\..*o" | \ xargs --no-run-if-empty -r rm; \ fi rm -f config.log config.status debian/rules build-arch /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ "debian/stamp-patched" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: if [ "debian/stamp-patched" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "debian/stamp-patched" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi make[1]: Entering directory `/«PKGBUILDDIR»' /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch /usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." /usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable dh_installdirs usr/lib/R/site-library echo "R:Depends=r-base-core (>= 2.15.1-4)" >> debian/r-bioc-biobase.substvars if test -f /usr/bin/xvfb-run; then \ xvfb-run -a \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library --clean \ . ; \ else \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library \ --clean . ;\ fi * installing *source* package 'Biobase' ... ** libs make[1]: Entering directory `/«PKGBUILDDIR»/src' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c anyMissing.c -o anyMissing.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c envir.c -o envir.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -shared -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR make[1]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Entering directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»/src' installing to /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'SW' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'aaMap' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'geneCov' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'geneCovariate' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'geneData' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'reporter' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'sample.ExpressionSet' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'sample.MultiSet' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'sample.eSet' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'sample.exprSet.1' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'sample.exprSet' not found Warning in utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) : data set 'seD' not found ** installing vignettes 'BiobaseDevelopment.Rnw' 'Bioconductor.Rnw' 'ExpressionSetIntroduction.Rnw' 'HowTo.Rnw' 'Qviews.Rnw' 'esApply.Rnw' ** testing if installed package can be loaded * DONE (Biobase) rm -vf /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library/R.css \ /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/COPYING \ /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/LICENSE.txt if test -f debian/overrides; then \ install -d /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/share/lintian/overrides ; \ install -m 0644 debian/overrides \ /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/share/lintian/overrides/r-bioc-biobase; \ fi Adding cdbs dependencies to debian/r-bioc-biobase.substvars dh_installdirs -pr-bioc-biobase echo "R:Depends=r-base-core (>= 2.15.1~)" >> debian/r-bioc-biobase.substvars dh_installdocs -pr-bioc-biobase ./NEWS dh_installexamples -pr-bioc-biobase dh_installman -pr-bioc-biobase dh_installinfo -pr-bioc-biobase dh_installmenu -pr-bioc-biobase dh_installcron -pr-bioc-biobase dh_installinit -pr-bioc-biobase dh_installdebconf -pr-bioc-biobase dh_installemacsen -pr-bioc-biobase dh_installcatalogs -pr-bioc-biobase dh_installpam -pr-bioc-biobase dh_installlogrotate -pr-bioc-biobase dh_installlogcheck -pr-bioc-biobase dh_installchangelogs -pr-bioc-biobase dh_installudev -pr-bioc-biobase dh_lintian -pr-bioc-biobase dh_bugfiles -pr-bioc-biobase dh_install -pr-bioc-biobase dh_link -pr-bioc-biobase dh_installmime -pr-bioc-biobase dh_installgsettings -pr-bioc-biobase dh_strip -pr-bioc-biobase dh_compress -pr-bioc-biobase dh_fixperms -pr-bioc-biobase dh_makeshlibs -pr-bioc-biobase dh_installdeb -pr-bioc-biobase dh_perl -pr-bioc-biobase dh_shlibdeps -pr-bioc-biobase dh_gencontrol -pr-bioc-biobase dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -pr-bioc-biobase dh_builddeb -pr-bioc-biobase -- -Z xz dpkg-deb: building package `r-bioc-biobase' in `../r-bioc-biobase_2.14.0-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../r-bioc-biobase_2.14.0-1_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 r-bioc-biobase-2.14.0 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120814-0943 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ r-bioc-biobase_2.14.0-1_armhf.changes: ────────────────────────────────────── Format: 1.8 Date: Wed, 02 Nov 2011 13:52:04 +0900 Source: r-bioc-biobase Binary: r-bioc-biobase Architecture: armhf Version: 2.14.0-1 Distribution: wheezy-staging Urgency: low Maintainer: buildd Changed-By: Charles Plessy Description: r-bioc-biobase - base functions for Bioconductor Changes: r-bioc-biobase (2.14.0-1) unstable; urgency=low . [cb6b786] Bioconductor release 2.9. [d70e490] Build-Depend on R >= 2.10 according to DESCRIPTION. [ae99e35] Include 7 digits of the commit id in the changelog entry. [33b5d47] Compress binary package with xz. Checksums-Sha1: 20a10249c275be1f08aa218e32b4872ca8d6a7e3 2283870 r-bioc-biobase_2.14.0-1_armhf.deb Checksums-Sha256: b4f7fb06c34d71f9e618ff7340ab608030b08794cf570faf8892475dc09fd536 2283870 r-bioc-biobase_2.14.0-1_armhf.deb Files: f9cd8d536d8b7361e32792d048cc3789 2283870 gnu-r optional r-bioc-biobase_2.14.0-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ r-bioc-biobase_2.14.0-1_armhf.deb ───────────────────────────────── new debian package, version 2.0. size 2283870 bytes: control archive=4949 bytes. 1221 bytes, 26 lines control 13314 bytes, 141 lines md5sums Package: r-bioc-biobase Version: 2.14.0-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 3007 Pre-Depends: dpkg (>= 1.15.6) Depends: libc6 (>= 2.13-28), r-base-core (>= 2.15.1~) Section: gnu-r Priority: optional Homepage: http://www.bioconductor.org Description: base functions for Bioconductor Biobase is part of the Bioconductor project, and is used by many other packages. Biobase contains standardized data structures to represent genomic data, and functions that are needed by many other packages or which replace R functions. . Bioconductor is a project to develop innovative software tools for use in computational biology. It is based on the R language. You should already be quite familiar with R before using Bioconductor. Bioconductor packages provide flexible interactive tools for carrying out a number of different computational tasks. . Most other Bioconductor packages are not packaged for Debian, but this packages provides in its Debian documentation instructions on how to install unofficial auto-generated Bioconductor packages for Debian and Ubuntu systems, that are prepared by members of the Debian Med team. drwxr-xr-x root/root 0 2012-08-14 09:42 ./ drwxr-xr-x root/root 0 2012-08-14 09:42 ./usr/ drwxr-xr-x root/root 0 2012-08-14 09:42 ./usr/share/ drwxr-xr-x root/root 0 2012-08-14 09:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-08-14 09:42 ./usr/share/doc/r-bioc-biobase/ -rw-r--r-- root/root 380 2012-08-14 09:40 ./usr/share/doc/r-bioc-biobase/changelog.Debian.gz -rw-r--r-- root/root 10574 2012-08-14 09:40 ./usr/share/doc/r-bioc-biobase/copyright -rw-r--r-- root/root 1380 2011-10-31 16:32 ./usr/share/doc/r-bioc-biobase/NEWS.gz -rw-r--r-- root/root 392 2012-08-14 09:40 ./usr/share/doc/r-bioc-biobase/README.Debian drwxr-xr-x root/root 0 2012-08-14 09:41 ./usr/lib/ drwxr-xr-x root/root 0 2012-08-14 09:41 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Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* cdbs* debhelper* file* fontconfig* fontconfig-config* gettext* gettext-base* gfortran* gfortran-4.6* groff-base* html2text* intltool-debian* libasprintf0c2* libblas-dev* libblas3* libbz2-dev* libcairo2* libcroco3* libdatrie1* libexpat1* libffi5* libfontconfig1* libfreetype6* libgettextpo0* libgfortran3* libglib2.0-0* libice6* libjbig0* libjpeg8* libjpeg8-dev* liblapack-dev* liblapack3* libmagic1* libncurses5-dev* libpango1.0-0* libpaper-utils* libpaper1* libpcre3* libpcre3-dev* libpcrecpp0* libpipeline1* libpixman-1-0* libpng12-0* libpng12-dev* libreadline-dev* libreadline6-dev* libsm6* libthai-data* libthai0* libtiff4* libtinfo-dev* libunistring0* libx11-6* libx11-data* libxau6* libxcb-render0* libxcb-shm0* libxcb1* libxdmcp6* libxext6* libxft2* libxml2* libxrender1* libxss1* libxt6* man-db* po-debconf* r-base-core* r-base-dev* sbuild-build-depends-core-dummy* sbuild-build-depends-r-bioc-biobase-dummy* tcl8.5* tk8.5* ttf-dejavu-core* unzip* x11-common* xdg-utils* zip* zlib1g-dev* 0 upgraded, 0 newly installed, 80 to remove and 6 not upgraded. After this operation, 112 MB disk space will be freed. (Reading database ... 14929 files and directories currently installed.) Removing sbuild-build-depends-r-bioc-biobase-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing r-base-dev ... Removing cdbs ... Removing file ... Removing r-base-core ... Purging configuration files for r-base-core ... Removing libpango1.0-0:armhf ... Purging configuration files for libpango1.0-0:armhf ... Removing fontconfig ... Purging configuration files for fontconfig ... Removing tk8.5 ... Purging configuration files for tk8.5 ... Removing libxft2:armhf ... Purging configuration files for libxft2:armhf ... Removing libcairo2:armhf ... Purging configuration files for libcairo2:armhf ... Removing libfontconfig1:armhf ... Purging configuration files for libfontconfig1:armhf ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing gfortran ... Removing gfortran-4.6 ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libasprintf0c2:armhf ... Removing liblapack-dev ... Removing libblas-dev ... Removing liblapack3 ... Purging configuration files for liblapack3 ... Removing libblas3 ... Removing libbz2-dev:armhf ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libthai0:armhf ... Purging configuration files for libthai0:armhf ... Removing libdatrie1:armhf ... Purging configuration files for libdatrie1:armhf ... Removing libexpat1:armhf ... Purging configuration files for libexpat1:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libfreetype6:armhf ... Purging configuration files for libfreetype6:armhf ... Removing libgettextpo0:armhf ... Removing libgfortran3:armhf ... Purging configuration files for libgfortran3:armhf ... Removing libxt6:armhf ... Purging configuration files for libxt6:armhf ... Removing libsm6:armhf ... Purging configuration files for libsm6:armhf ... Removing libice6:armhf ... Purging configuration files for libice6:armhf ... Removing libtiff4:armhf ... Purging configuration files for libtiff4:armhf ... Removing libjbig0:armhf ... Purging configuration files for libjbig0:armhf ... Removing libjpeg8-dev:armhf ... Removing libjpeg8:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libncurses5-dev ... Removing libpaper-utils ... Removing libpaper1:armhf ... Purging configuration files for libpaper1:armhf ... Removing libpcre3-dev ... Removing libpcrecpp0:armhf ... Purging configuration files for libpcrecpp0:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libpixman-1-0:armhf ... Purging configuration files for libpixman-1-0:armhf ... Removing libpng12-dev ... Removing libpng12-0:armhf ... Purging configuration files for libpng12-0:armhf ... Removing libreadline-dev:armhf ... Removing libreadline6-dev:armhf ... Removing libthai-data ... Removing libtinfo-dev:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxss1:armhf ... Purging configuration files for libxss1:armhf ... Removing libxrender1:armhf ... Purging configuration files for libxrender1:armhf ... Removing libxext6:armhf ... Purging configuration files for libxext6:armhf ... Removing libx11-6:armhf ... Purging configuration files for libx11-6:armhf ... Removing libx11-data ... Removing libxcb-shm0:armhf ... Purging configuration files for libxcb-shm0:armhf ... Removing libxcb-render0:armhf ... Purging configuration files for libxcb-render0:armhf ... Removing libxcb1:armhf ... Purging configuration files for libxcb1:armhf ... Removing libxau6:armhf ... Purging configuration files for libxau6:armhf ... Removing libxdmcp6:armhf ... Purging configuration files for libxdmcp6:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... Removing tcl8.5 ... Purging configuration files for tcl8.5 ... Removing ttf-dejavu-core ... Removing unzip ... Purging configuration files for unzip ... Removing x11-common ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of stop. Purging configuration files for x11-common ... Removing xdg-utils ... Removing zip ... Removing zlib1g-dev:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 9048 Build-Time: 136 Distribution: wheezy-staging Host Architecture: armhf Install-Time: 155 Job: r-bioc-biobase_2.14.0-1 Machine Architecture: armhf Package: r-bioc-biobase Package-Time: 315 Source-Version: 2.14.0-1 Space: 9048 Status: successful Version: 2.14.0-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120814-0943 Build needed 00:05:15, 9048k disc space