Raspbian Package Auto-Building

Build log for tophat (2.0.8-1) on armhf

tophat2.0.8-1armhf → 2013-07-08 03:11:54

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testwandboard

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║ tophat 2.0.8-1 (armhf)                                     08 Jul 2013 02:44 ║
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Package: tophat
Version: 2.0.8-1
Source Version: 2.0.8-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/tophat-UY2kGA/tophat-2.0.8' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/tophat-UY2kGA' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-125292e6-c89e-4194-bdca-5e31fbce66f6' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6661 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7794 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.5 MB in 44s (328 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
─────────

Checking available source versions...

Download source files with APT
──────────────────────────────

Reading package lists...
Building dependency tree...
NOTICE: 'tophat' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/tophat.git
Need to get 435 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main tophat 2.0.8-1 (dsc) [2135 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main tophat 2.0.8-1 (tar) [427 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main tophat 2.0.8-1 (diff) [5717 B]
Fetched 435 kB in 0s (520 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-gah3SO/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...
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/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 ... 11383 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~), seqan-dev (>= 1.3~), libboost-thread-dev, help2man
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, libbam-dev (>= 0.1.16), zlib1g-dev, dh-autoreconf, python (>= 2.6.6-3~), seqan-dev (>= 1.3~), libboost-thread-dev, help2man
dpkg-deb: building package `sbuild-build-depends-tophat-dummy' in `/«BUILDDIR»/resolver-3UWHo8/apt_archive/sbuild-build-depends-tophat-dummy.deb'.
OK
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install tophat build dependencies (apt-based resolver)                       │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file
  gettext gettext-base groff-base help2man intltool-debian libasprintf0c2
  libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0
  libboost-serialization1.49-dev libboost-serialization1.49.0
  libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0
  libboost1.49-dev libcroco3 libexpat1 libffi6 libglib2.0-0 libicu48 libmagic1
  libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
  libsigsegv2 libsqlite3-0 libssl1.0.0 libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-minimal python2.7 python2.7-minimal
  seqan-dev zlib1g-dev
Suggested packages:
  autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist
  whois vacation dh-make gettext-doc groff libboost1.49-doc
  libboost-chrono1.49-dev libboost-filesystem1.49-dev
  libboost-graph-parallel1.49-dev libboost-graph1.49-dev
  libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev
  libboost-mpi1.49-dev libboost-program-options1.49-dev
  libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev
  libboost-signals1.49-dev libboost-system1.49-dev libboost-test1.49-dev
  libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml
  docbook-xsl default-jdk fop libtool-doc automaken gfortran
  fortran95-compiler gcj less www-browser libmail-box-perl python-doc
  python-tk python2.7-doc binfmt-support
Recommended packages:
  autopoint curl wget lynx-cur libasprintf-dev libgettextpo-dev
  libglib2.0-data shared-mime-info libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autotools-dev bsdmainutils debhelper dh-autoreconf file
  gettext gettext-base groff-base help2man intltool-debian libasprintf0c2
  libbam-dev libboost-date-time1.49-dev libboost-date-time1.49.0
  libboost-serialization1.49-dev libboost-serialization1.49.0
  libboost-thread-dev libboost-thread1.49-dev libboost-thread1.49.0
  libboost1.49-dev libcroco3 libexpat1 libffi6 libglib2.0-0 libicu48 libmagic1
  libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
  libsigsegv2 libsqlite3-0 libssl1.0.0 libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-minimal python2.7 python2.7-minimal
  sbuild-build-depends-tophat-dummy seqan-dev zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 6 not upgraded.
Need to get 34.0 MB/34.0 MB of archives.
After this operation, 180 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
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Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.3-7 [867 kB]
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Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.7.17-1 [436 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-2 [836 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.5-5 [520 kB]
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Get:12 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.1-2build1 [1895 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-3 [117 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libicu48 armhf 4.8.1.1-12 [4494 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.2.1-1 [131 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.54 [36.4 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.5-5 [2413 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libsigsegv2 armhf 2.9-4 [28.4 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main m4 armhf 1.4.16-5 [245 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.5-5 [229 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.5-2 [43.4 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.5-2 [19.6 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.5-2 [181 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main autoconf all 2.69-1 [589 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main autotools-dev all 20130515.1 [73.0 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main automake all 1:1.13.3-1 [758 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.2.1-1 [1932 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20130605 [709 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libtool armhf 2.4.2-1.2 [617 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main dh-autoreconf all 7 [15.3 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.43.2 [100 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libbam-dev armhf 0.1.19-1 [110 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libboost1.49-dev armhf 1.49.0-4 [8940 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libboost-date-time1.49.0 armhf 1.49.0-4 [43.5 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libboost-serialization1.49.0 armhf 1.49.0-4 [188 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libboost-serialization1.49-dev armhf 1.49.0-4 [341 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libboost-date-time1.49-dev armhf 1.49.0-4 [51.9 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libboost-thread1.49.0 armhf 1.49.0-4 [60.9 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libboost-thread1.49-dev armhf 1.49.0-4 [74.2 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libboost-thread-dev armhf 1.49.0.1 [2744 B]
Get:47 http://172.17.0.1/private/ jessie-staging/main seqan-dev all 1.3.1-1 [2442 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.2.4-1) ...
Setting up libssl1.0.0:armhf (1.0.1e-2+rpi1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
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 man-db (2.6.3-7) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.2.1-1) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libsqlite3-0:armhf (3.7.17-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-2) ...
Setting up libpython2.7-minimal (2.7.5-5) ...
Setting up python2.7-minimal (2.7.5-5) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.1-2build1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libexpat1:armhf (2.1.0-3) ...
Setting up libicu48:armhf (4.8.1.1-12) ...
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Setting up automake (1:1.13.3-1) ...
update-alternatives: using /usr/bin/automake-1.13 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.18.2.1-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20130605) ...
Setting up libtool (2.4.2-1.2) ...
Setting up dh-autoreconf (7) ...
Setting up help2man (1.43.2) ...
Setting up libbam-dev (0.1.19-1) ...
Setting up libboost1.49-dev (1.49.0-4) ...
Setting up libboost-date-time1.49.0 (1.49.0-4) ...
Setting up libboost-serialization1.49.0 (1.49.0-4) ...
Setting up libboost-serialization1.49-dev (1.49.0-4) ...
Setting up libboost-date-time1.49-dev (1.49.0-4) ...
Setting up libboost-thread1.49.0 (1.49.0-4) ...
Setting up libboost-thread1.49-dev (1.49.0-4) ...
Setting up libboost-thread-dev (1.49.0.1) ...
Setting up seqan-dev (1.3.1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up sbuild-build-depends-tophat-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.0.35-wand5.2 armhf (armv7l)
Toolchain package versions: binutils_2.23.52.20130612-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-6+rpi1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 autoconf_2.69-1 automake_1:1.13.3-1 autotools-dev_20130515.1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130612-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.4 build-essential_11.6 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-1 cpp_4:4.6.3-8 cpp-4.6_4.6.4-2+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130605 debianutils_4.3.4 dh-autoreconf_7 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.4-2+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-2+rpi1 gcc-4.6-base_4.6.4-2+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8-base_4.8.0-7+rpi1 gettext_0.18.2.1-1 gettext-base_0.18.2.1-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 help2man_1.43.2 hostname_3.13 initramfs-tools_0.113 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf0c2_0.18.2.1-1 libattr1_1:2.4.47-1 libbam-dev_0.1.19-1 libblkid1_2.20.1-5.4 libboost-date-time1.49-dev_1.49.0-4 libboost-date-time1.49.0_1.49.0-4 libboost-serialization1.49-dev_1.49.0-4 libboost-serialization1.49.0_1.49.0-4 libboost-thread-dev_1.49.0.1 libboost-thread1.49-dev_1.49.0-4 libboost-thread1.49.0_1.49.0-4 libboost1.49-dev_1.49.0-4 libbz2-1.0_1.0.6-4 libc-bin_2.17-6+rpi1 libc-dev-bin_2.17-6+rpi1 libc6_2.17-6+rpi1 libc6-dev_2.17-6+rpi1 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdbus-1-3_1.6.12-1 libdpkg-perl_1.16.10 libexpat1_2.1.0-3 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.0-7+rpi1 libgdbm3_1.8.3-12 libglib2.0-0_2.36.1-2build1 libgmp10_2:5.1.2+dfsg-1 libgomp1_4.8.0-7+rpi1 libicu48_4.8.1.1-12 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.1+b1 libnih1_1.0.3-4.1+b1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libpython-stdlib_2.7.5-2 libpython2.7-minimal_2.7.5-5 libpython2.7-stdlib_2.7.5-5 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libsigsegv2_2.9-4 libslang2_2.2.4-15 libsqlite3-0_3.7.17-1 libss2_1.42.5-1.1 libssl1.0.0_1.0.1e-2+rpi1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 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+20130608-1 libtool_2.4.2-1.2 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.9.1+dfsg1-2 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 m4_1.4.16-5 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.3-7 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.4 mountall_2.48 multiarch-support_2.17-6+rpi1 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.8-6+deb8u1 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 python_2.7.5-2 python-minimal_2.7.5-2 python2.7_2.7.5-5 python2.7-minimal_2.7.5-5 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.9 seqan-dev_1.3.1-1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-6 tzdata_2013c-2 udev_175-7.2 util-linux_2.20.1-5.4 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Mar  2 11:50:39 2013 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./tophat_2.0.8-1.dsc
dpkg-source: info: extracting tophat in tophat-2.0.8
dpkg-source: info: unpacking tophat_2.0.8.orig.tar.gz
dpkg-source: info: unpacking tophat_2.0.8-1.debian.tar.gz
dpkg-source: info: applying fix_includes_path.patch
dpkg-source: info: applying bashism_in_shell_script.patch

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-125292e6-c89e-4194-bdca-5e31fbce66f6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
previous=N
runlevel=2

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package tophat
dpkg-buildpackage: source version 2.0.8-1
 dpkg-source --before-build tophat-2.0.8
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean --with autoreconf
   dh_testdir
   dh_auto_clean
   dh_autoreconf_clean
   dh_clean
	rm -f debian/tophat.substvars
	rm -f debian/tophat.*.debhelper
	rm -rf debian/tophat/
	rm -f debian/*.debhelper.log
	rm -f debian/files
	find .  \( \( -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} \; \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
	rm -f *-stamp
 debian/rules build-arch
dh build-arch --with autoreconf
   dh_testdir -a
   dh_autoreconf -a
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} \; > debian/autoreconf.before
	autoreconf -f -i
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
sh: 1: svnversion: not found
configure.ac:35: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:35: the top level
/usr/share/automake-1.13/am/library.am: warning: 'libgc.a': linking libraries using a non-POSIX
/usr/share/automake-1.13/am/library.am: archiver requires 'AM_PROG_AR' in 'configure.ac'
src/Makefile.am:556:   while processing library 'libgc.a'
/usr/share/automake-1.13/am/library.am: warning: 'libtophat.a': linking libraries using a non-POSIX
/usr/share/automake-1.13/am/library.am: archiver requires 'AM_PROG_AR' in 'configure.ac'
src/Makefile.am:556:   while processing library 'libtophat.a'
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} \; > debian/autoreconf.after
   dh_auto_configure -a
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) mawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for boostlib >= 1.38.0... yes
checking for bamlib... yes
checking build system type... arm-unknown-linux-gnueabihf
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-mt... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for ANSI C header files... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking for an ANSI C-conforming const... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for gzread in -lz... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for memset... yes
checking for strdup... yes
checking for strrchr... yes
checking for strtol... yes
checking for strsep... yes
checking host system type... arm-unknown-linux-gnueabihf
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) none
checking dependency style of g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode

-- tophat 2.0.8 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3
  Linker flags:        -Wl,-z,relro
  GCC version:         gcc (Debian 4.6.4-2+rpi1) 4.6.4
  Host System type:    arm-unknown-linux-gnueabihf
  Install prefix:      /usr
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <cole@cs.umd.edu, infphilo@umiacs.umd.edu> with questions and bug reports.

   dh_auto_build -a
	make -j1
make[1]: Entering directory `/«PKGBUILDDIR»'
make  all-recursive
make[2]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o reads.o reads.cpp
In file included from reads.h:17:0,
                 from reads.cpp:25:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
gcc -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -c alphabet.c
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o bwt_map.o bwt_map.cpp
In file included from bwt_map.cpp:26:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
bwt_map.cpp: In function 'bool spliceCigar(std::vector<CigarOp>&, const std::vector<CigarOp>&, std::vector<bool>, int&, int, int, CigarOpCode, int&)':
bwt_map.cpp:705:9: warning: variable 'prev_opcode' set but not used [-Wunused-but-set-variable]
bwt_map.cpp:706:9: warning: variable 'prev_oplen' set but not used [-Wunused-but-set-variable]
bwt_map.cpp: In member function 'virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)':
bwt_map.cpp:1112:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable]
bwt_map.cpp:1118:7: warning: variable 'num_hits' set but not used [-Wunused-but-set-variable]
bwt_map.cpp: In member function 'virtual bool SplicedBAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)':
bwt_map.cpp:1481:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable]
bwt_map.cpp:1486:8: warning: variable 'spliced_alignment' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o common.o common.cpp
In file included from common.cpp:26:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
common.cpp: In function 'void str_appendInt(std::string&, int64_t)':
common.cpp:441:28: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int64_t {aka long long int}' [-Wformat]
common.cpp: In function 'void str_appendUInt(std::string&, uint64_t)':
common.cpp:447:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat]
common.cpp: In member function 'std::string GBamRecord::seqData(std::string*)':
common.cpp:1245:8: warning: variable 'mate_num' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o junctions.o junctions.cpp
In file included from junctions.cpp:15:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o insertions.o insertions.cpp
In file included from insertions.cpp:33:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o deletions.o deletions.cpp
In file included from deletions.cpp:14:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o fusions.o fusions.cpp
In file included from fusions.cpp:32:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o align_status.o align_status.cpp
In file included from align_status.cpp:19:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o fragments.o fragments.cpp
In file included from bwt_map.h:22:0,
                 from fragments.cpp:15:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o tokenize.o tokenize.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o inserts.o inserts.cpp
In file included from bwt_map.h:22:0,
                 from inserts.cpp:17:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o qual.o qual.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o bam_merge_impl.o bam_merge_impl.cpp
In file included from bam_merge.h:11:0,
                 from bam_merge_impl.cpp:1:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o utils.o utils.cpp
In file included from utils.h:16:0,
                 from utils.cpp:20:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
utils.cpp: In function 'bool calculate_offsets(const std::vector<std::basic_string<char> >&, std::vector<long long unsigned int>&, std::vector<std::vector<long long int> >&)':
utils.cpp:41:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o coverage.o coverage.cpp
In file included from coverage.h:16:0,
                 from coverage.cpp:15:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
coverage.cpp: In member function 'void Coverage::print_info() const':
coverage.cpp:226:96: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::map<int, std::vector<signed char> >::size_type {aka unsigned int}' [-Wformat]
coverage.cpp:226:96: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat]
coverage.cpp:230:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat]
coverage.cpp: In member function 'void Coverage::print_info(int, const std::vector<signed char>&) const':
coverage.cpp:250:60: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<signed char>::size_type {aka unsigned int}' [-Wformat]
rm -f libtophat.a
ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o 
ranlib libtophat.a
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o GBase.o GBase.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o codons.o codons.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o gdna.o gdna.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o GStr.o GStr.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o GFaSeqGet.o GFaSeqGet.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o gff.o gff.cpp
rm -f libgc.a
ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o 
ranlib libgc.a
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o prep_reads.o prep_reads.cpp
In file included from prep_reads.cpp:20:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro   -Wl,-z,relro -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o GTFToFasta.o GTFToFasta.cpp
In file included from GTFToFasta.h:27:0,
                 from GTFToFasta.cpp:7:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o FastaTools.o FastaTools.cpp
In file included from FastaTools.h:26:0,
                 from FastaTools.cpp:8:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o gtf_to_fasta GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o fix_map_ordering.o fix_map_ordering.cpp
In file included from fix_map_ordering.cpp:16:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o fix_map_ordering fix_map_ordering.o ../src/libtophat.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o bam2fastx.o bam2fastx.cpp
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o segment_juncs.o segment_juncs.cpp
In file included from segment_juncs.cpp:37:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
segment_juncs.cpp: In member function 'void SegmentSearchWorker::operator()()':
segment_juncs.cpp:4752:27: warning: variable 'last_read_id' set but not used [-Wunused-but-set-variable]
segment_juncs.cpp: In function 'void driver(std::istream&, FILE*, FILE*, FILE*, FILE*, std::string&, std::string&, std::vector<std::basic_string<char> >&, std::string&, std::string&, std::vector<std::basic_string<char> >&)':
segment_juncs.cpp:5190:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::set<Junction>::size_type {aka unsigned int}' [-Wformat]
segment_juncs.cpp:5208:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::set<Insertion>::size_type {aka unsigned int}' [-Wformat]
/tmp/ccXmib8X.s: Assembler messages:
/tmp/ccXmib8X.s:11770: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccXmib8X.s:11799: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccXmib8X.s:11836: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro -L/usr/lib  -Wl,-z,relro -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread-mt  -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o gtf_juncs.o gtf_juncs.cpp
In file included from gtf_juncs.cpp:23:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o gtf_juncs gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o juncs_db.o juncs_db.cpp
In file included from juncs_db.cpp:32:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o juncs_db juncs_db.o ../src/libtophat.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o long_spanning_reads.o long_spanning_reads.cpp
In file included from long_spanning_reads.cpp:36:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
/tmp/ccVl5tI8.s: Assembler messages:
/tmp/ccVl5tI8.s:4085: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:4114: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:4151: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:6801: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:6829: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:6866: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:7021: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:7049: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:7086: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:8285: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:8302: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:8338: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:9327: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:9344: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:9380: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103129: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103147: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103183: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103342: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103362: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103399: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103534: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103552: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103589: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103691: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103709: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccVl5tI8.s:103746: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro -L/usr/lib  -Wl,-z,relro -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread-mt  -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o bam_merge.o bam_merge.cpp
In file included from bam_merge.h:11:0,
                 from bam_merge.cpp:1:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o bam_merge bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o map2gtf.o map2gtf.cpp
In file included from bwt_map.h:22:0,
                 from map2gtf.h:31,
                 from map2gtf.cpp:6:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o map2gtf map2gtf.o ../src/libtophat.a libgc.a -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o tophat_reports.o tophat_reports.cpp
In file included from tophat_reports.cpp:36:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
tophat_reports.cpp: In constructor 'MultipleBAMReader::MultipleBAMReader(ReadTable&, RefSequenceTable&, const std::vector<std::basic_string<char> >&, long int, long int)':
tophat_reports.cpp:1685:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat]
/tmp/ccmWWice.s: Assembler messages:
/tmp/ccmWWice.s:7765: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:7794: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:7831: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:85571: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:85588: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:85624: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:91481: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:91499: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccmWWice.s:91536: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro -L/usr/lib  -Wl,-z,relro -o tophat_reports tophat_reports.o ../src/libtophat.a  -lboost_thread-mt  -lbam -lz 
g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o sam_juncs.o sam_juncs.cpp
In file included from sam_juncs.cpp:19:0:
common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
sam_juncs.cpp: In function 'void driver(FILE*)':
sam_juncs.cpp:106:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::map<Junction, JunctionStats>::size_type {aka unsigned int}' [-Wformat]
g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -Wl,-z,relro  -Wl,-z,relro -o sam_juncs sam_juncs.o ../src/libtophat.a -lbam -lz 
sed -e 's|__PREFIX__|/usr|' tophat2.in > tophat2
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
   dh_auto_test -a
	make -j1 check
make[1]: Entering directory `/«PKGBUILDDIR»'
Making check in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
 fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
   dh_testroot -a
   dh_prep -a
	rm -f debian/tophat.substvars
	rm -f debian/tophat.*.debhelper
	rm -rf debian/tophat/
   debian/rules override_dh_auto_install
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_install
	install -d debian/tophat
	make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tophat AM_UPDATE_INFO_DIR=no
make[2]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'
make[4]: Entering directory `/«PKGBUILDDIR»/src'
 /bin/mkdir -p '/«PKGBUILDDIR»/debian/tophat/usr/bin'
  /usr/bin/install -c prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/«PKGBUILDDIR»/debian/tophat/usr/bin'
 /bin/mkdir -p '/«PKGBUILDDIR»/debian/tophat/usr/bin'
 /usr/bin/install -c tophat2 '/«PKGBUILDDIR»/debian/tophat/usr/bin'
 /bin/mkdir -p '/«PKGBUILDDIR»/debian/tophat/usr/bin'
 /usr/bin/install -c contig_to_chr_coords tophat bed_to_juncs sra_to_solid tophat-fusion-post '/«PKGBUILDDIR»/debian/tophat/usr/bin'
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[4]: Entering directory `/«PKGBUILDDIR»'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
# try to create man pages whereever possible
mkdir -p /«PKGBUILDDIR»/debian/tophat/usr/share/man/man1
help2man --no-info --no-discard-stderr  -h "" \
	    --name='converts bam directly into fastx' \
	    --version-string="2.0.8" \
	         /«PKGBUILDDIR»/debian/tophat/usr/bin/bam2fastx > /«PKGBUILDDIR»/debian/tophat/usr/share/man/man1/bam2fastx.1
help2man --no-info --no-discard-stderr \
	    --name='TopHat maps short sequences from spliced transcripts to whole genomes' \
	    --version-string="2.0.8" \
	         /«PKGBUILDDIR»/debian/tophat/usr/bin/tophat > /«PKGBUILDDIR»/debian/tophat/usr/share/man/man1/tophat.1
make[1]: Leaving directory `/«PKGBUILDDIR»'
   dh_installdocs -a
	install -g 0 -o 0 -d debian/tophat/usr/share/doc/tophat
	cp -a NEWS debian/tophat/usr/share/doc/tophat
	cp -a README debian/tophat/usr/share/doc/tophat
	chown -R 0:0 debian/tophat/usr/share/doc
	chmod -R go=rX debian/tophat/usr/share/doc
	chmod -R u\+rw debian/tophat/usr/share/doc
	install -g 0 -o 0 -m 644 -p debian/copyright debian/tophat/usr/share/doc/tophat/copyright
   dh_installchangelogs -a
	install -o 0 -g 0 -p -m644 debian/changelog debian/tophat/usr/share/doc/tophat/changelog.Debian
   dh_installman -a
	man --recode UTF-8 ./bam2fastx\.1 > bam2fastx\.1\.new
	chmod 644 bam2fastx.1.new
	mv -f bam2fastx.1.new bam2fastx.1
	man --recode UTF-8 ./tophat\.1 > tophat\.1\.new
	chmod 644 tophat.1.new
	mv -f tophat.1.new tophat.1
   dh_perl -a
   dh_link -a
   dh_compress -a
	cd debian/tophat
	chmod a-x usr/share/man/man1/bam2fastx.1 usr/share/man/man1/tophat.1 usr/share/doc/tophat/NEWS usr/share/doc/tophat/changelog.Debian
	gzip -9nf usr/share/man/man1/bam2fastx.1 usr/share/man/man1/tophat.1 usr/share/doc/tophat/NEWS usr/share/doc/tophat/changelog.Debian
	cd '/«PKGBUILDDIR»'
   dh_fixperms -a
	find debian/tophat  -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
	find debian/tophat ! -type l  -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/tophat/usr/share/doc -type f  ! -regex 'debian/tophat/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat/usr/share/doc -type d  -print0 2>/dev/null | xargs -0r chmod 755
	find debian/tophat/usr/share/man debian/tophat/usr/man/ debian/tophat/usr/X11*/man/ -type f  -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \)  -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat/usr/include -type f  -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat/usr/share/applications -type f  -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat -perm -5 -type f \( -name '*.cmxs' \)  -print0 2>/dev/null | xargs -0r chmod 644
	find debian/tophat/usr/lib/perl5 debian/tophat/usr/share/perl5 -type f -perm -5 -name '*.pm'  -print0 2>/dev/null | xargs -0r chmod a-X
	find debian/tophat/usr/bin -type f  -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/tophat/usr/lib -type f -name '*.ali'  -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_strip -a
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/prep_reads
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/gtf_to_fasta
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/fix_map_ordering
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/bam2fastx
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/segment_juncs
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/gtf_juncs
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/juncs_db
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/long_spanning_reads
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/bam_merge
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/map2gtf
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/tophat_reports
	strip --remove-section=.comment --remove-section=.note debian/tophat/usr/bin/sam_juncs
   dh_makeshlibs -a
	rm -f debian/tophat/DEBIAN/shlibs
   dh_shlibdeps -a
	install -o 0 -g 0 -d debian/tophat/DEBIAN
	dpkg-shlibdeps -Tdebian/tophat.substvars debian/tophat/usr/bin/prep_reads debian/tophat/usr/bin/gtf_to_fasta debian/tophat/usr/bin/fix_map_ordering debian/tophat/usr/bin/bam2fastx debian/tophat/usr/bin/segment_juncs debian/tophat/usr/bin/gtf_juncs debian/tophat/usr/bin/juncs_db debian/tophat/usr/bin/long_spanning_reads debian/tophat/usr/bin/bam_merge debian/tophat/usr/bin/map2gtf debian/tophat/usr/bin/tophat_reports debian/tophat/usr/bin/sam_juncs
   dh_installdeb -a
   dh_gencontrol -a
	echo misc:Depends= >> debian/tophat.substvars
	dpkg-gencontrol -ldebian/changelog -Tdebian/tophat.substvars -Pdebian/tophat
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
	chmod 644 debian/tophat/DEBIAN/control
	chown 0:0 debian/tophat/DEBIAN/control
   dh_md5sums -a
	(cd debian/tophat >/dev/null ; find . -type f  ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
	chmod 644 debian/tophat/DEBIAN/md5sums
	chown 0:0 debian/tophat/DEBIAN/md5sums
   debian/rules override_dh_builddeb
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_builddeb -- -Z xz
	dpkg-deb -Z xz --build debian/tophat ..
dpkg-deb: building package `tophat' in `../tophat_2.0.8-1_armhf.deb'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../tophat_2.0.8-1_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 tophat-2.0.8
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130708-0307

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


tophat_2.0.8-1_armhf.changes:
─────────────────────────────

Format: 1.8
Date: Sat, 02 Mar 2013 12:38:32 +0100
Source: tophat
Binary: tophat
Architecture: armhf
Version: 2.0.8-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
Description: 
 tophat     - fast splice junction mapper for RNA-Seq reads
Changes: 
 tophat (2.0.8-1) unstable; urgency=low
 .
   * Imported Upstream version 2.0.8
Checksums-Sha1: 
 d2d84296d1031cc2a9b518aa26b37091d0ac331b 525836 tophat_2.0.8-1_armhf.deb
Checksums-Sha256: 
 90851bb3dccd485845443e8198e43c1a5a17d7340d5c94cb7b75873e905c846a 525836 tophat_2.0.8-1_armhf.deb
Files: 
 611e3c79679179d69edb73999a0d3e80 525836 science optional tophat_2.0.8-1_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


tophat_2.0.8-1_armhf.deb
────────────────────────

 new debian package, version 2.0.
 size 525836 bytes: control archive=1479 bytes.
     943 bytes,    19 lines      control              
    1382 bytes,    24 lines      md5sums              
 Package: tophat
 Version: 2.0.8-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3114
 Pre-Depends: dpkg (>= 1.15.6~)
 Depends: libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.3.3), python (>= 2.6.6-3~), bowtie2 | bowtie
 Suggests: cufflinks, bowtie
 Section: science
 Priority: optional
 Homepage: http://tophat.cbcb.umd.edu/
 Description: fast splice junction mapper for RNA-Seq reads
  TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra
  high-throughput short read aligner Bowtie, and then analyzes the
  mapping results to identify splice junctions between exons.
  TopHat is a collaborative effort between the University of Maryland
  Center for Bioinformatics and Computational Biology and the
  University of California, Berkeley Departments of Mathematics and
  Molecular and Cell Biology.

drwxr-xr-x root/root         0 2013-07-08 03:06 ./
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/bin/
-rwxr-xr-x root/root       241 2013-07-08 03:06 ./usr/bin/tophat2
-rwxr-xr-x root/root      4631 2013-07-08 03:06 ./usr/bin/contig_to_chr_coords
-rwxr-xr-x root/root    168280 2013-07-08 03:06 ./usr/bin/tophat
-rwxr-xr-x root/root      1817 2013-07-08 03:06 ./usr/bin/bed_to_juncs
-rwxr-xr-x root/root       716 2013-07-08 03:06 ./usr/bin/sra_to_solid
-rwxr-xr-x root/root    105504 2013-07-08 03:06 ./usr/bin/tophat-fusion-post
-rwxr-xr-x root/root    201712 2013-07-08 03:06 ./usr/bin/prep_reads
-rwxr-xr-x root/root    221820 2013-07-08 03:06 ./usr/bin/gtf_to_fasta
-rwxr-xr-x root/root    135596 2013-07-08 03:06 ./usr/bin/fix_map_ordering
-rwxr-xr-x root/root    109688 2013-07-08 03:06 ./usr/bin/bam2fastx
-rwxr-xr-x root/root    447468 2013-07-08 03:06 ./usr/bin/segment_juncs
-rwxr-xr-x root/root    205296 2013-07-08 03:06 ./usr/bin/gtf_juncs
-rwxr-xr-x root/root    164344 2013-07-08 03:06 ./usr/bin/juncs_db
-rwxr-xr-x root/root    385764 2013-07-08 03:06 ./usr/bin/long_spanning_reads
-rwxr-xr-x root/root    135584 2013-07-08 03:06 ./usr/bin/bam_merge
-rwxr-xr-x root/root    217624 2013-07-08 03:06 ./usr/bin/map2gtf
-rwxr-xr-x root/root    430812 2013-07-08 03:06 ./usr/bin/tophat_reports
-rwxr-xr-x root/root    238092 2013-07-08 03:06 ./usr/bin/sam_juncs
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/share/
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/share/man/
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/share/man/man1/
-rw-r--r-- root/root       490 2013-07-08 03:06 ./usr/share/man/man1/bam2fastx.1.gz
-rw-r--r-- root/root      1898 2013-07-08 03:06 ./usr/share/man/man1/tophat.1.gz
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/share/doc/
drwxr-xr-x root/root         0 2013-07-08 03:06 ./usr/share/doc/tophat/
-rw-r--r-- root/root      1432 2013-02-21 19:56 ./usr/share/doc/tophat/README
-rw-r--r-- root/root      3652 2013-03-02 11:39 ./usr/share/doc/tophat/copyright
-rw-r--r-- root/root      2998 2013-02-21 19:56 ./usr/share/doc/tophat/NEWS.gz
-rw-r--r-- root/root      1714 2013-03-02 11:39 ./usr/share/doc/tophat/changelog.Debian.gz


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 53301
Build-Time: 749
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 526
Job: tophat_2.0.8-1
Machine Architecture: armhf
Package: tophat
Package-Time: 1342
Source-Version: 2.0.8-1
Space: 53301
Status: successful
Version: 2.0.8-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20130708-0307
Build needed 00:22:22, 53301k disc space