sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ gff2aplot 2.0-7 (armhf) 15 May 2012 04:35 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: gff2aplot Version: 2.0-7 Source Version: 2.0-7 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/gff2aplot-l4dFDi/gff2aplot-2.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/gff2aplot-l4dFDi' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-bd2f5059-f523-4088-838c-cbbbd989d054' 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: 'gff2aplot' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/gff2aplot/trunk/ Need to get 340 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main gff2aplot 2.0-7 (dsc) [1390 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main gff2aplot 2.0-7 (tar) [328 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main gff2aplot 2.0-7 (diff) [10.6 kB] Fetched 340 kB in 0s (4963 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-fMbGdv/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 13 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 ... 10670 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 (>= 9) Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9) dpkg-deb: building package `sbuild-build-depends-gff2aplot-dummy' in `/«BUILDDIR»/resolver-rrykHn/apt_archive/sbuild-build-depends-gff2aplot-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install gff2aplot 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 gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-gff2aplot-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 19 newly installed, 0 to remove and 13 not upgraded. Need to get 0 B/9373 kB of archives. After this operation, 24.2 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10670 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 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 libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.2-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... 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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 sbuild-build-depends-gff2aplot-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 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 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 libdpkg-perl_1.16.2 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 libglib2.0-0_2.32.2-1 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi 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_5.9-7 libncursesw5_5.9-7 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_1:8.30-5 libpipeline1_1.2.1-1 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 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 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 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 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-7 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 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gff2aplot-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_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed May 2 08:25:19 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./gff2aplot_2.0-7.dsc dpkg-source: info: extracting gff2aplot in gff2aplot-2.0 dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz dpkg-source: info: unpacking gff2aplot_2.0-7.debian.tar.gz dpkg-source: info: applying 02-blat2gff.diff dpkg-source: info: applying 03-parseblast.diff dpkg-source: info: applying use-dpkg-buildflags.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-bd2f5059-f523-4088-838c-cbbbd989d054 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package gff2aplot dpkg-buildpackage: source version 2.0-7 dpkg-source --before-build gff2aplot-2.0 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -f src/ali2gff/ali2gff bin/ali2gff make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' ### ### RUNNING MAKEFILE ### ### Tue May 15 11:36:44 UTC 2012 -- buildd ### ### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl" ### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl" ### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl" ### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl" ### Making ALI2GFF... make[2]: Entering directory `/«PKGBUILDDIR»/src/ali2gff' ali2gff.c: In function 'main': ali2gff.c:88:8: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] ali2gff.c: In function 'processMumfile': ali2gff.c:837:18: warning: 'fyb' may be used uninitialized in this function [-Wuninitialized] ali2gff.c:836:18: warning: 'fxb' may be used uninitialized in this function [-Wuninitialized] ali2gff.c:728:12: warning: 'score' may be used uninitialized in this function [-Wuninitialized] ali2gff.c: In function 'processSimfile': ali2gff.c:1068:15: warning: 'yrev' may be used uninitialized in this function [-Wuninitialized] ali2gff.c:1060:41: warning: 'yseqLen_4' may be used uninitialized in this function [-Wuninitialized] ali2gff.c:1060:15: warning: 'xseqLen_4' may be used uninitialized in this function [-Wuninitialized] make[2]: Leaving directory `/«PKGBUILDDIR»/src/ali2gff' `./src/ali2gff/ali2gff' -> `./bin/ali2gff' mode of `bin/gff2aplot.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x) mode of `bin/parseblast.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x) mode of `bin/blat2gff.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x) mode of `bin/sim2gff.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x) ### ### MAKEFILE DONE... ### make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a make[1]: Entering directory `/«PKGBUILDDIR»' ### SORRY !!! Tests were not implemented yet... make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done make[1]: Leaving directory `/«PKGBUILDDIR»' 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 dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `gff2aplot' in `../gff2aplot_2.0-7_armhf.deb'. dpkg-genchanges -B -mbuildd >../gff2aplot_2.0-7_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 gff2aplot-2.0 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120515-0437 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ gff2aplot_2.0-7_armhf.changes: ────────────────────────────── Format: 1.8 Date: Tue, 01 May 2012 22:37:01 +0200 Source: gff2aplot Binary: gff2aplot Architecture: armhf Version: 2.0-7 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript Changes: gff2aplot (2.0-7) unstable; urgency=low . * debian/upstream: Added citation information * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs-Svn - Removed cdbs+quilt from Build-Depends * debian/copyright: Rewritten to DEP5 * debian/patches/use-dpkg-buildflags.patch: Use build flags from environment to enable hardening * debhelper 9 (control+compat) Checksums-Sha1: 5987f66a3d1815de4c298519609813e98a9cf176 331972 gff2aplot_2.0-7_armhf.deb Checksums-Sha256: 07d7f24573b5345a394a0c7c91e638a22c60a6e43b4a74c8f8a99755000a4691 331972 gff2aplot_2.0-7_armhf.deb Files: 67ecafa53eb13ae121d7802db68c0a78 331972 science optional gff2aplot_2.0-7_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ gff2aplot_2.0-7_armhf.deb ───────────────────────── new debian package, version 2.0. size 331972 bytes: control archive= 3288 bytes. 2778 bytes, 47 lines control 5009 bytes, 58 lines md5sums Package: gff2aplot Version: 2.0-7 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 628 Depends: libc6 (>= 2.13-28), perl Suggests: postscript-viewer, gff2ps Section: science Priority: optional Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Description: pair-wise alignment-plots for genomic sequences in PostScript A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot: * Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets. * All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file. * Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement. * All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients. * Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes. * The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error. * gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape. * You can draw different alignments on same alignment plot and distinguish them by using different colors for each. * Shape dictionary has been expanded, so that further feature shapes are now available (see manual). * Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows to show color pseudo-blending when horizontal and vertical ribbons overlap. drwxr-xr-x root/root 0 2012-05-15 04:37 ./ drwxr-xr-x root/root 0 2012-05-15 04:36 ./usr/ drwxr-xr-x root/root 0 2012-05-15 04:37 ./usr/share/ drwxr-xr-x root/root 0 2012-05-15 04:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-15 04:37 ./usr/share/doc/gff2aplot/ -rw-r--r-- root/root 66844 2003-06-05 08:45 ./usr/share/doc/gff2aplot/GFF2APLOT_MANUAL.ps.gz drwxr-xr-x root/root 0 2012-05-15 04:37 ./usr/share/doc/gff2aplot/examples/ drwxr-xr-x root/root 0 2012-05-15 04:37 ./usr/share/doc/gff2aplot/examples/mhcregion/ -rw-r--r-- root/root 55 2003-06-05 08:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2labels.rc -rw-r--r-- root/root 797 2003-06-05 08:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2.rc -rw-r--r-- root/root 10206 2003-06-05 08:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs.fa.gz -rw-r--r-- root/root 4496 2003-06-05 08:45 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Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 3372 Build-Time: 63 Distribution: testing Install-Time: 59 Job: gff2aplot_2.0-7 Package: gff2aplot Package-Time: 139 Source-Version: 2.0-7 Space: 3372 Status: successful Version: 2.0-7 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120515-0437 Build needed 00:02:19, 3372k disc space