bowtie →
1.0.0-3 →
armhf → 2013-05-21 01:28:54
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on debian-armhf
╔══════════════════════════════════════════════════════════════════════════════╗
║ bowtie 1.0.0-3 (armhf) 21 May 2013 00:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bowtie
Version: 1.0.0-3
Source Version: 1.0.0-3
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bowtie-5tB6DL/bowtie-1.0.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bowtie-5tB6DL' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-397128d5-487a-4993-8f86-92a55e230c1b' 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 [6553 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7529 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.1 MB in 36s (388 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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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 7607 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-3 (dsc) [2137 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-3 (tar) [7594 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bowtie 1.0.0-3 (diff) [10.6 kB]
Fetched 7607 kB in 7s (1050 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-e_ZaSN/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 0 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 ... 11288 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man, seqan-dev (>= 1.3)
Filtered Build-Depends: 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-h7rY5L/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 libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libpcre3 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0
libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
po-debconf sbuild-build-depends-bowtie-dummy seqan-dev
0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded.
Need to get 11.7 MB/11.7 MB of archives.
After this operation, 43.7 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpcre3 armhf 1:8.30-5 [242 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.1-1 [35.0 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 5.11-2 [199 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [822 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libffi5 armhf 3.0.10-3+b3 [22.9 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.33.12+really2.32.4-5 [1689 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.6-2 [119 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libgettextpo0 armhf 0.18.1.1-9 [130 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.3 [207 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.21-9 [1071 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.2-1 [1027 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main file armhf 5.11-2 [51.4 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.1.1-9 [138 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main html2text armhf 1.3.2a-15 [98.5 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.1.1-9 [1879 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20120909 [705 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.40.10 [96.0 kB]
Get:22 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 11.7 MB in 12s (939 kB/s)
Selecting previously unselected package libpcre3:armhf.
(Reading database ... 11288 files and directories currently installed.)
Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ...
Selecting previously unselected package libpipeline1:armhf.
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_5.11-2_armhf.deb) ...
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Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-2_armhf.deb) ...
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Selecting previously unselected package sbuild-build-depends-bowtie-dummy.
Unpacking sbuild-build-depends-bowtie-dummy (from .../sbuild-build-depends-bowtie-dummy.deb) ...
Setting up libpcre3:armhf (1:8.30-5) ...
Setting up libpipeline1:armhf (1.2.1-1) ...
Setting up libasprintf0c2:armhf (0.18.1.1-9) ...
Setting up libmagic1:armhf (5.11-2) ...
Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:armhf (3.0.10-3+b3) ...
Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.6-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libgettextpo0:armhf (0.18.1.1-9) ...
Setting up bsdmainutils (9.0.3) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up groff-base (1.21-9) ...
Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
Setting up file (5.11-2) ...
Setting up gettext-base (0.18.1.1-9) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20120909) ...
Setting up help2man (1.40.10) ...
Setting up seqan-dev (1.3.1-1) ...
Setting up sbuild-build-depends-bowtie-dummy (0.invalid.0) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.9.1-imx4 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-14+rpi1 gcc-4.6_4.6.3-14+rpi1 libc6-dev_2.13-38+rpi2 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 binutils_2.22-8 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.3 build-essential_11.5+b1 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_4.6.3-14+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20120909 debianutils_4.3.2 diffutils_1:3.2-6 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_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-14+rpi1 gcc-4.6-base_4.6.3-14+rpi1 gcc-4.7-base_4.7.2-5+rpi1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 help2man_1.40.10 hostname_3.11 html2text_1.3.2a-15 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_2.2.51-8 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38+rpi2 libc-dev-bin_2.13-38+rpi2 libc6_2.13-38+rpi2 libc6-dev_2.13-38+rpi2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.8-1 libdpkg-perl_1.16.10 libffi5_3.0.10-3+b3 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5+rpi1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5+rpi1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libnih-dbus1_1.0.3-4.1 libnih1_1.0.3-4.1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-9 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libprocps0_1:3.3.3-3 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+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_5.9-10 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 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_2.3.1-92 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.3 mountall_2.46 multiarch-support_2.13-38+rpi2 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.5.1-5 po-debconf_1.0.16+nmu2 procps_1:3.3.3-3 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_4.2.1-10 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-0.1 tzdata_2013b-2 udev_175-7.2 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Wed Apr 24 12:26:38 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_1.0.0-3.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_1.0.0-3.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-397128d5-487a-4993-8f86-92a55e230c1b
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 53109 22
SSH_CONNECTION=192.168.1.2 53109 192.168.1.45 22
SSH_TTY=/dev/pts/1
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1369081280.146676-2082782793
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bowtie
dpkg-buildpackage: source version 1.0.0-3
dpkg-buildpackage: source changed by Ognyan Kulev <ogi@debian.org>
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
dh_compress -a
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_1.0.0-3_armhf.deb'.
dpkg-genchanges -B >../bowtie_1.0.0-3_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build bowtie-1.0.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130521-0128
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bowtie_1.0.0-3_armhf.changes:
─────────────────────────────
Format: 1.8
Date: Wed, 24 Apr 2013 15:15:37 +0300
Source: bowtie
Binary: bowtie bowtie-examples
Architecture: armhf
Version: 1.0.0-3
Distribution: jessie-staging
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.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 (1.0.0-3) unstable; urgency=low
.
* New patch no_hash_style_both_for_mips.patch.
This fixes build errors on mips and mipsel.
Checksums-Sha1:
11ffd9e2990ae673307b47bd267703e57b6a7fb7 1318798 bowtie_1.0.0-3_armhf.deb
Checksums-Sha256:
c1f6a287c85f8da0101d12c0333d6feddefcba1c412a13cf8d1a2e67801e7c46 1318798 bowtie_1.0.0-3_armhf.deb
Files:
281d46d0d58e9186fbab2668a6421900 1318798 science extra bowtie_1.0.0-3_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bowtie_1.0.0-3_armhf.deb
────────────────────────
new debian package, version 2.0.
size 1318798 bytes: control archive=1287 bytes.
996 bytes, 21 lines control
1076 bytes, 17 lines md5sums
Package: bowtie
Version: 1.0.0-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2706
Depends: libc6 (>= 2.13-28), 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 2013-05-21 01:28 ./
drwxr-xr-x root/root 0 2013-05-21 01:28 ./usr/
drwxr-xr-x root/root 0 2013-05-21 01:28 ./usr/share/
drwxr-xr-x root/root 0 2013-05-21 01:28 ./usr/share/man/
drwxr-xr-x root/root 0 2013-05-21 01:28 ./usr/share/man/man1/
-rw-r--r-- root/root 2643 2013-05-21 01:28 ./usr/share/man/man1/bowtie.1.gz
-rw-r--r-- root/root 1118 2013-05-21 01:28 ./usr/share/man/man1/bowtie-build.1.gz
-rw-r--r-- root/root 882 2013-05-21 01:28 ./usr/share/man/man1/bowtie-inspect.1.gz
drwxr-xr-x root/root 0 2013-05-21 01:28 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-05-21 01:28 ./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 1044 2013-04-24 12:20 ./usr/share/doc/bowtie/changelog.Debian.gz
drwxr-xr-x root/root 0 2013-05-21 01:28 ./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 2013-05-21 01:28 ./usr/bin/
-rwxr-xr-x root/root 502392 2013-05-21 01:28 ./usr/bin/bowtie
-rwxr-xr-x root/root 228380 2013-05-21 01:28 ./usr/bin/bowtie-build
-rwxr-xr-x root/root 176380 2013-05-21 01:28 ./usr/bin/bowtie-inspect
-rwxr-xr-x root/root 502872 2013-05-21 01:28 ./usr/bin/bowtie-build-debug
-rwxr-xr-x root/root 1026716 2013-05-21 01:28 ./usr/bin/bowtie-debug
-rwxr-xr-x root/root 176380 2013-05-21 01:28 ./usr/bin/bowtie-inspect-debug
lrwxrwxrwx root/root 0 2013-05-21 01:28 ./usr/share/man/man1/bowtie-inspect-debug.1.gz -> bowtie-inspect.1.gz
lrwxrwxrwx root/root 0 2013-05-21 01:28 ./usr/share/man/man1/bowtie-build-debug.1.gz -> bowtie-build.1.gz
lrwxrwxrwx root/root 0 2013-05-21 01:28 ./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: 45528
Build-Time: 1711
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 150
Job: bowtie_1.0.0-3
Machine Architecture: armhf
Package: bowtie
Package-Time: 1925
Source-Version: 1.0.0-3
Space: 45528
Status: successful
Version: 1.0.0-3
────────────────────────────────────────────────────────────────────────────────
Finished at 20130521-0128
Build needed 00:32:05, 45528k disc space