bowtie →
1.0.0-5 →
armhf → 2013-06-17 11:33:44
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ bowtie 1.0.0-5 (armhf) 17 Jun 2013 11:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bowtie
Version: 1.0.0-5
Source Version: 1.0.0-5
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bowtie-AknTM8/bowtie-1.0.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bowtie-AknTM8' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-aefa08e0-13d4-40ab-b7e3-abedffb64af3' 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 [6639 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7568 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.2 MB in 38s (369 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...
Reading state information...
NOTICE: 'bowtie' packaging is maintained in the 'Svn' version control system at:
svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk
Need to get 7606 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-5 (dsc) [2114 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-5 (tar) [7594 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-5 (diff) [10.3 kB]
Fetched 7606 kB in 11s (653 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-sWYkYT/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 3 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 ... 11338 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), help2man, seqan-dev (>= 1.3)
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), help2man, seqan-dev (>= 1.3)
dpkg-deb: building package `sbuild-build-depends-bowtie-dummy' in `/«BUILDDIR»/resolver-hE4wzl/apt_archive/sbuild-build-depends-bowtie-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bowtie 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 help2man
html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi6
libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf seqan-dev
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 help2man
html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi6
libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bowtie-dummy
seqan-dev
0 upgraded, 24 newly installed, 0 to remove and 3 not upgraded.
Need to get 11.1 MB/11.1 MB of archives.
After this operation, 41.8 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.3-1 [35.8 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.3-6 [867 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [822 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.1-2build1 [1895 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libgettextpo0 armhf 0.18.1.1-10 [131 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.1.1-10 [130 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main html2text armhf 1.3.2a-16 [97.6 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libasprintf-dev armhf 0.18.1.1-10 [26.7 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libgettextpo-dev armhf 0.18.1.1-10 [160 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.1.1-10 [1721 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20120909 [705 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.41.2 [100 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main seqan-dev all 1.3.1-1 [2442 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 11.1 MB in 12s (901 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11338 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.3-1_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-6_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7+nmu1_armhf.deb) ...
Selecting previously unselected package libffi6:armhf.
Unpacking libffi6:armhf (from .../libffi6_3.0.13-4_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.36.1-2build1_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.8-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ...
Selecting previously unselected package libgettextpo0:armhf.
Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_1%3a5.14-2_armhf.deb) ...
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Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-16_armhf.deb) ...
Selecting previously unselected package libasprintf-dev:armhf.
Unpacking libasprintf-dev:armhf (from .../libasprintf-dev_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package libgettextpo-dev:armhf.
Unpacking libgettextpo-dev:armhf (from .../libgettextpo-dev_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package help2man.
Unpacking help2man (from .../help2man_1.41.2_armhf.deb) ...
Selecting previously unselected package seqan-dev.
Unpacking seqan-dev (from .../seqan-dev_1.3.1-1_all.deb) ...
Selecting previously unselected package sbuild-build-depends-bowtie-dummy.
Unpacking sbuild-build-depends-bowtie-dummy (from .../sbuild-build-depends-bowtie-dummy.deb) ...
Setting up libpipeline1:armhf (1.2.3-1) ...
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 (2.6.3-6) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
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 libunistring0:armhf (0.9.3-5) ...
Setting up libgettextpo0:armhf (0.18.1.1-10) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.1.1-10) ...
Setting up html2text (1.3.2a-16) ...
Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20120909) ...
Setting up help2man (1.41.2) ...
Setting up seqan-dev (1.3.1-1) ...
Setting up sbuild-build-depends-bowtie-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.9.4-imx4 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-3 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 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.22-8 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-0.1 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_9.20120909 debianutils_4.3.4 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_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.5-1.1 help2man_1.41.2 hostname_3.12 html2text_1.3.2a-16 initramfs-tools_0.112 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 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.4 libbz2-1.0_1.0.6-4 libc-bin_2.17-3 libc-dev-bin_2.17-3 libc6_2.17-3 libc6-dev_2.17-3 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_5.1.29-5 libdbus-1-3_1.6.10-1 libdpkg-perl_1.16.10 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.0-7+rpi1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.36.1-2build1 libgmp10_2:5.1.2+dfsg-1 libgomp1_4.8.0-7+rpi1 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 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130504-1 libncursesw5_5.9+20130504-1 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_1.2.3-1 libprocps0_1:3.3.4-2 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 libslang2_2.2.4-15 libss2_1.42.5-1.1 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+20130504-1 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.3-6 mawk_1.3.3-17 mount_2.20.1-5.4 multiarch-support_2.17-3 ncurses-base_5.9+20130504-1 ncurses-bin_5.9+20130504-1 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 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-bowtie-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.7 seqan-dev_1.3.1-1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-5 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu May 30 06:58:03 2013 UTC using RSA key ID 36D33D07
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bowtie_1.0.0-5.dsc
dpkg-source: info: extracting bowtie in bowtie-1.0.0
dpkg-source: info: unpacking bowtie_1.0.0.orig.tar.gz
dpkg-source: info: unpacking bowtie_1.0.0-5.debian.tar.gz
dpkg-source: info: applying use-dpkg-buildflags.patch
dpkg-source: info: applying use_debian_seqan.patch
dpkg-source: info: applying seqan-fix-setBegin-call.patch
dpkg-source: info: applying seqan-rename-ChunkPool.patch
dpkg-source: info: applying seqan-rename-fill-to-resize.patch
dpkg-source: info: applying disable_bits_flag.patch
dpkg-source: info: applying no_hash_style_both_for_mips.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=root
LS_OPTIONS=--color=auto
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-aefa08e0-13d4-40ab-b7e3-abedffb64af3
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 53797 22
SSH_CONNECTION=192.168.1.2 53797 192.168.1.45 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1371250784.150246-1803625542
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bowtie
dpkg-buildpackage: source version 1.0.0-5
dpkg-source --before-build bowtie-1.0.0
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 .bowtie*
dh_auto_clean
make[2]: Entering directory `/«PKGBUILDDIR»'
rm -f bowtie-build bowtie bowtie-inspect bowtie-build-debug bowtie-debug bowtie-inspect-debug \
bowtie_prof \
bowtie-build.exe bowtie.exe bowtie-inspect.exe bowtie-build-debug.exe bowtie-debug.exe bowtie-inspect-debug.exe bowtie_prof.exe \
bowtie-src.zip bowtie-bin.zip
rm -f core.*
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
/usr/bin/make allall
make[2]: Entering directory `/«PKGBUILDDIR»'
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-I /usr/include/seqan \
-o bowtie-build ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \
-lpthread
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-I /usr/include/seqan \
-o bowtie ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-lpthread
g++ -O3 \
-DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
-I /usr/include/seqan -I . \
-o bowtie-inspect bowtie_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
-lpthread
g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
-I /usr/include/seqan \
-o bowtie-build-debug ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \
-lpthread
g++ -O0 -g3 \
-DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
-I /usr/include/seqan \
-o bowtie-debug ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-lpthread
g++ -O0 -g3 \
-DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
-I /usr/include/seqan -I . \
-o bowtie-inspect-debug bowtie_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
-lpthread
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory `/«PKGBUILDDIR»'
help2man --name="ultrafast memory-efficient short read aligner" --no-info \
/«PKGBUILDDIR»/bowtie > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie.1
help2man --name="building a colorspace index for bowtie" --no-info \
/«PKGBUILDDIR»/bowtie-build > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie-build.1
help2man --name="extracts information from a bowtie index" --no-info \
/«PKGBUILDDIR»/bowtie-inspect > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie-inspect.1
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
debian/rules override_dh_compress
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_compress -X.ebwt
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `bowtie' in `../bowtie_1.0.0-5_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../bowtie_1.0.0-5_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 bowtie-1.0.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130617-1133
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bowtie_1.0.0-5_armhf.changes:
─────────────────────────────
Format: 1.8
Date: Thu, 30 May 2013 09:41:25 +0300
Source: bowtie
Binary: bowtie bowtie-examples
Architecture: armhf
Version: 1.0.0-5
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Ognyan Kulev <ogi@debian.org>
Description:
bowtie - Ultrafast memory-efficient short read aligner
bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al
Changes:
bowtie (1.0.0-5) unstable; urgency=low
.
* Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
instead of override_dh_fixperms in debian/rules.
Checksums-Sha1:
5204e2c15746e4e102ed98a2a1046b21c453541b 1319588 bowtie_1.0.0-5_armhf.deb
Checksums-Sha256:
94b71ddcee4ae8d4862cac04db1275e5cace5798bec92e372e55cd8ab148ac9d 1319588 bowtie_1.0.0-5_armhf.deb
Files:
db188ee338383b6ec5cc48f860153683 1319588 science extra bowtie_1.0.0-5_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bowtie_1.0.0-5_armhf.deb
────────────────────────
new debian package, version 2.0.
size 1319588 bytes: control archive=1286 bytes.
992 bytes, 21 lines control
1076 bytes, 17 lines md5sums
Package: bowtie
Version: 1.0.0-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2706
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0)
Suggests: bowtie-examples
Section: science
Priority: extra
Homepage: http://bowtie-bio.sourceforge.net/
Description: Ultrafast memory-efficient short read aligner
This package addresses the problem to interpret the results from the
latest (2010) DNA sequencing technologies. Those will yield fairly
short stretches and those cannot be interpreted directly. It is the
challenge for tools like Bowtie to give a chromosomal location to the
short stretches of DNA sequenced per run.
.
Bowtie aligns short DNA sequences (reads) to the human genome at a rate
of over 25 million 35-bp reads per hour. Bowtie indexes the genome with
a Burrows-Wheeler index to keep its memory footprint small: typically
about 2.2 GB for the human genome (2.9 GB for paired-end).
drwxr-xr-x root/root 0 2013-06-17 11:33 ./
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/man/
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/man/man1/
-rw-r--r-- root/root 2652 2013-06-17 11:33 ./usr/share/man/man1/bowtie.1.gz
-rw-r--r-- root/root 1126 2013-06-17 11:33 ./usr/share/man/man1/bowtie-build.1.gz
-rw-r--r-- root/root 890 2013-06-17 11:33 ./usr/share/man/man1/bowtie-inspect.1.gz
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/doc/bowtie/
-rw-r--r-- root/root 107525 2013-04-09 15:30 ./usr/share/doc/bowtie/manual.html
-rw-r--r-- root/root 4182 2013-03-08 09:06 ./usr/share/doc/bowtie/style.css
-rw-r--r-- root/root 2543 2013-04-18 09:04 ./usr/share/doc/bowtie/copyright
-rw-r--r-- root/root 11332 2013-04-09 15:30 ./usr/share/doc/bowtie/NEWS.gz
-rw-r--r-- root/root 21534 2013-04-09 15:42 ./usr/share/doc/bowtie/MANUAL.gz
-rw-r--r-- root/root 2576 2013-03-08 09:06 ./usr/share/doc/bowtie/TUTORIAL.gz
-rw-r--r-- root/root 1277 2013-05-30 06:41 ./usr/share/doc/bowtie/changelog.Debian.gz
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/share/doc-base/
-rw-r--r-- root/root 1010 2013-04-18 09:04 ./usr/share/doc-base/bowtie
drwxr-xr-x root/root 0 2013-06-17 11:33 ./usr/bin/
-rwxr-xr-x root/root 502396 2013-06-17 11:33 ./usr/bin/bowtie
-rwxr-xr-x root/root 228384 2013-06-17 11:33 ./usr/bin/bowtie-build
-rwxr-xr-x root/root 176384 2013-06-17 11:33 ./usr/bin/bowtie-inspect
-rwxr-xr-x root/root 502876 2013-06-17 11:33 ./usr/bin/bowtie-build-debug
-rwxr-xr-x root/root 1026720 2013-06-17 11:33 ./usr/bin/bowtie-debug
-rwxr-xr-x root/root 176384 2013-06-17 11:33 ./usr/bin/bowtie-inspect-debug
lrwxrwxrwx root/root 0 2013-06-17 11:33 ./usr/share/man/man1/bowtie-inspect-debug.1.gz -> bowtie-inspect.1.gz
lrwxrwxrwx root/root 0 2013-06-17 11:33 ./usr/share/man/man1/bowtie-build-debug.1.gz -> bowtie-build.1.gz
lrwxrwxrwx root/root 0 2013-06-17 11:33 ./usr/share/man/man1/bowtie-debug.1.gz -> bowtie.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 45524
Build-Time: 1760
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 139
Job: bowtie_1.0.0-5
Machine Architecture: armhf
Package: bowtie
Package-Time: 1971
Source-Version: 1.0.0-5
Space: 45524
Status: successful
Version: 1.0.0-5
────────────────────────────────────────────────────────────────────────────────
Finished at 20130617-1133
Build needed 00:32:51, 45524k disc space