bedtools →
2.19.1-1 →
armhf → 2014-03-31 05:51:36
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testwandboard
╔══════════════════════════════════════════════════════════════════════════════╗
║ bedtools 2.19.1-1 (armhf) 31 Mar 2014 05:23 ║
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Package: bedtools
Version: 2.19.1-1
Source Version: 2.19.1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bedtools-9AFbd_/bedtools-2.19.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bedtools-9AFbd_' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-c4ce5d0e-e0e2-4847-8a39-c1543eb067e0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7344 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8511 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/bedtools.git
Need to get 4161 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main bedtools 2.19.1-1 (dsc) [2027 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main bedtools 2.19.1-1 (tar) [4150 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bedtools 2.19.1-1 (diff) [8664 B]
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Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-JsviBG/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 20 not upgraded.
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Selecting previously unselected package sbuild-build-depends-core-dummy.
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
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), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
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), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-uRJ4Cr/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
quilt zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi6 libglib2.0-0
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
quilt sbuild-build-depends-bedtools-dummy zlib1g-dev
0 upgraded, 33 newly installed, 0 to remove and 20 not upgraded.
Need to get 13.8 MB/13.8 MB of archives.
After this operation, 42.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.6-2 [20.3 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1f-1 [809 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 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 2.6.6-1 [961 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.17-1 [225 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.8.3.1-1 [350 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.6-8 [346 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.6-8 [1092 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-12 [17.4 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.38.2-5 [2073 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 2.1.0-4 [117 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.17-1 [55.3 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.54 [36.4 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.6-8 [1827 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.6-8 [239 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.5-5 [43.1 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.5-5 [19.8 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.5-5 [180 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.122 [81.4 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main diffstat armhf 1.58-1 [27.2 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main quilt all 0.61-1 [345 kB]
Get:32 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 (1.2.6-2) ...
Setting up libssl1.0.0:armhf (1.0.1f-1) ...
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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
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Setting up libmagic1:armhf (1:5.17-1) ...
Setting up libsqlite3-0:armhf (3.8.3.1-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libpython2.7-minimal:armhf (2.7.6-8) ...
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Setting up libffi6:armhf (3.0.13-12) ...
Setting up libglib2.0-0:armhf (2.38.2-5) ...
No schema files found: doing nothing.
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Setting up libexpat1:armhf (2.1.0-4) ...
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Setting up file (1:5.17-1) ...
Setting up gettext-base (0.18.3.2-1) ...
Setting up mime-support (3.54) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
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Setting up intltool-debian (0.35.0+20060710.1) ...
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Processing triggers for libc-bin (2.18-4) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.6_4.6.4-5+rpi1 g++-4.8_4.8.2-16 gcc-4.6_4.6.4-5+rpi1 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libstdc++6-4.6-dev_4.6.4-5+rpi1 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.15.4 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.122 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-2 cpp-4.6_4.6.4-5+rpi1 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffstat_1.58-1 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-1 findutils_4.4.2-7 g++_4:4.8.2-2 g++-4.6_4.6.4-5+rpi1 g++-4.8_4.8.2-16 gcc_4:4.8.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-5+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libarchive-extract-perl_0.72-1 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libexpat1_2.1.0-4 libffi6_3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgdbm3_1.8.3-12 libglib2.0-0_2.38.2-5 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblog-message-simple-perl_0.10-1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-1 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpcre3_1:8.31-2 libpipeline1_1.2.6-2 libpod-latex-perl_0.61-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libpython-stdlib_2.7.5-5 libpython2.7-minimal_2.7.6-8 libpython2.7-stdlib_2.7.6-8 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsqlite3-0_3.8.3.1-1 libss2_1.42.9-3 libssl1.0.0_1.0.1f-1 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libstdc++6-4.6-dev_4.6.4-5+rpi1 libswitch-perl_2.16-2 libterm-ui-perl_0.42-1 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1 libudev0_175-7.2 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.6-1 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 python_2.7.5-5 python-minimal_2.7.5-5 python2.7_2.7.6-8 python2.7-minimal_2.7.6-8 quilt_0.61-1 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 udev_204-7 util-linux_2.20.1-5.6 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 Fri Mar 21 07:21:13 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bedtools_2.19.1-1.dsc
dpkg-source: info: extracting bedtools in bedtools-2.19.1
dpkg-source: info: unpacking bedtools_2.19.1.orig.tar.gz
dpkg-source: info: unpacking bedtools_2.19.1-1.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying debian-changes
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-c4ce5d0e-e0e2-4847-8a39-c1543eb067e0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
dpkg-buildpackage: source version 2.19.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build bedtools-2.19.1
dpkg-buildpackage: host architecture armhf
dpkg-source: info: using options from bedtools-2.19.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
test -x debian/rules
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
make[1]: Entering directory `/«PKGBUILDDIR»'
* Cleaning-up BamTools API
* Cleaning up.
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
rm -rf debian/bedtools/
rm -f debian/bedtools-test.substvars
rm -f debian/bedtools-test.*.debhelper
rm -rf debian/bedtools-test/
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
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
if [ -d "." ]; then \
cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch debian-changes
Restoring src/slopBed/slopBed.cpp
Restoring src/slopBed/slopBed.h
Restoring src/utils/fileType/fileType.cpp
Restoring test/map/test-map.sh
Restoring test/reldist/test-reldist.sh
Restoring test/slop/test-slop.sh
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Applying patch debian-changes
patching file src/slopBed/slopBed.cpp
patching file src/slopBed/slopBed.h
patching file src/utils/fileType/fileType.cpp
patching file test/map/test-map.sh
patching file test/reldist/test-reldist.sh
patching file test/slop/test-slop.sh
Now at patch debian-changes
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
make[1]: Entering directory `/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.19.1
CURRENT_VERSION =
Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
- Building in src/utils/BinTree
* compiling BinTree.cpp
- Building in src/utils/version
* compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
- Building in src/utils/Contexts
* compiling ContextBase.cpp
* compiling ContextIntersect.cpp
* compiling ContextMap.cpp
* compiling ContextSample.cpp
- Building in src/utils/FileRecordTools
- Building in FileReaders
* compiling FileReader.cpp
* compiling SingleLineDelimTransferBuffer.cpp
* compiling SingleLineDelimTextFileReader.cpp
* compiling BamFileReader.cpp
* compiling BufferedStreamMgr.cpp
* compiling InputStreamMgr.cpp
- Building in Records
* compiling RecordMgr.cpp
* compiling Record.cpp
* compiling Bed3Interval.cpp
* compiling Bed4Interval.cpp
* compiling BedGraphInterval.cpp
* compiling Bed5Interval.cpp
* compiling Bed6Interval.cpp
* compiling BedPlusInterval.cpp
* compiling Bed12Interval.cpp
* compiling BamRecord.cpp
* compiling VcfRecord.cpp
* compiling GffRecord.cpp
* compiling RecordKeyList.cpp
* compiling BlockMgr.cpp
* compiling FileRecordMgr.cpp
- Building in src/utils/general
* compiling QuickString.cpp
* compiling ParseTools.cpp
* compiling PushBackStreamBuf.cpp
* compiling CompressionTools.cpp
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
* compiling FileRecordTypeChecker.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
- Building in src/utils/KeyListOps
* compiling KeyListOps.cpp
* compiling KeyListOpsMethods.cpp
- Building in src/utils/NewChromsweep
* compiling NewChromsweep.cpp
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/utils/tabFile
* compiling tabFile.cpp
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
* compiling SamHeader.cpp
* compiling SamProgram.cpp
* compiling SamProgramChain.cpp
* compiling SamReadGroup.cpp
* compiling SamReadGroupDictionary.cpp
* compiling SamSequence.cpp
* compiling SamSequenceDictionary.cpp
* compiling BamHeader_p.cpp
* compiling BamMultiReader_p.cpp
* compiling BamRandomAccessController_p.cpp
* compiling BamReader_p.cpp
* compiling BamWriter_p.cpp
* compiling BamIndexFactory_p.cpp
* compiling BamStandardIndex_p.cpp
* compiling BamToolsIndex_p.cpp
* compiling BamDeviceFactory_p.cpp
* compiling BamFile_p.cpp
* compiling BamFtp_p.cpp
* compiling BamHttp_p.cpp
* compiling BamPipe_p.cpp
* compiling BgzfStream_p.cpp
* compiling ByteArray_p.cpp
* compiling HostAddress_p.cpp
* compiling HostInfo_p.cpp
* compiling HttpHeader_p.cpp
* compiling ILocalIODevice_p.cpp
* compiling RollingBuffer_p.cpp
* compiling TcpSocketEngine_p.cpp
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
* linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
* compiling BamAncillary.cpp
- Building in src/utils/BlockedIntervals
* compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:29:12: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
length = NULL;
^
Fasta.cpp:32:15: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
line_blen = NULL;
^
Fasta.cpp:33:15: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
line_len = NULL;
^
* compiling split.cpp
- Building in src/utils/VectorOps
* compiling VectorOps.cpp
- Building in src/utils/GenomeFile
* compiling GenomeFile.cpp
GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
long c2;
^
* compiling NewGenomeFile.cpp
- Building in src/utils/RecordOutputMgr
* compiling RecordOutputMgr.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
bool haveTitles = false;
^
* compiling annotateBed.cpp
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
bool useAlignmentScore = false;
^
- Building in src/bamToFastq
* compiling bamToFastqMain.cpp
bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
bool haveFastq2 = false;
^
* compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
bool haveMapQual = false;
^
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
bool haveMaxDistance = false;
^
* compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- Building in src/expand
* compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
bool haveColumns = false;
^
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
bool haveOps = true;
^
- Building in src/intersectFile
* compiling intersectMain.cpp
* compiling intersectFile.cpp
- Building in src/jaccard
* compiling jaccardMain.cpp
* compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- Building in src/mapFile
* compiling mapMain.cpp
* compiling mapFile.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
bool haveMaxDistance = false;
^
* compiling mergeBed.cpp
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
bool haveBed = false;
^
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
bool haveBams = false;
^
multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^
* compiling multiIntersectBed.cpp
- Building in src/nekSandbox1
* compiling nekSandboxMain.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
CHRPOS spanLength = 0;
^
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
int spanLength = 0;
^
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling pairToPair.cpp
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
bool found1 = false;
^
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
bool found2 = false;
^
- Building in src/randomBed
* compiling randomBedMain.cpp
* compiling randomBed.cpp
- Building in src/regressTest
compiling RegressTest.cpp
compiling regressTestMain.cpp
- Building in src/reldist
* compiling reldistMain.cpp
* compiling reldist.cpp
reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()':
reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=]
(float) freqItr->second / (float) _tot_queries);
^
reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=]
- Building in src/sampleFile
* compiling sampleMain.cpp
* compiling SampleFile.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- Building in src/subtractBed
* compiling subtractMain.cpp
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
bool haveFraction = false;
^
* compiling tagBam.cpp
- Building in src/unionBedGraphs
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
bool haveFiles = false;
^
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
bool haveGenome = false;
^
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
bool haveFiller = true;
^
* compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
make[1]: Leaving directory `/«PKGBUILDDIR»'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
rm -rf debian/bedtools/
rm -f debian/bedtools-test.substvars
rm -f debian/bedtools-test.*.debhelper
rm -rf debian/bedtools-test/
dh_installdirs -A
install -d debian/bedtools
install -d debian/bedtools-test
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
cp -a README.md debian/bedtools/usr/share/doc/bedtools
chown -R 0:0 debian/bedtools/usr/share/doc
chmod -R go=rX debian/bedtools/usr/share/doc
chmod -R u\+rw debian/bedtools/usr/share/doc
install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
install -d debian/bedtools/usr/bin
cp -a ./bin/annotateBed debian/bedtools/usr/bin/
cp -a ./bin/bamToBed debian/bedtools/usr/bin/
cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
cp -a ./bin/bedToBam debian/bedtools/usr/bin/
cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
cp -a ./bin/bedtools debian/bedtools/usr/bin/
cp -a ./bin/closestBed debian/bedtools/usr/bin/
cp -a ./bin/clusterBed debian/bedtools/usr/bin/
cp -a ./bin/complementBed debian/bedtools/usr/bin/
cp -a ./bin/coverageBed debian/bedtools/usr/bin/
cp -a ./bin/expandCols debian/bedtools/usr/bin/
cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
cp -a ./bin/flankBed debian/bedtools/usr/bin/
cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
cp -a ./bin/getOverlap debian/bedtools/usr/bin/
cp -a ./bin/groupBy debian/bedtools/usr/bin/
cp -a ./bin/intersectBed debian/bedtools/usr/bin/
cp -a ./bin/linksBed debian/bedtools/usr/bin/
cp -a ./bin/mapBed debian/bedtools/usr/bin/
cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
cp -a ./bin/mergeBed debian/bedtools/usr/bin/
cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
cp -a ./bin/nucBed debian/bedtools/usr/bin/
cp -a ./bin/pairToBed debian/bedtools/usr/bin/
cp -a ./bin/pairToPair debian/bedtools/usr/bin/
cp -a ./bin/randomBed debian/bedtools/usr/bin/
cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
cp -a ./bin/slopBed debian/bedtools/usr/bin/
cp -a ./bin/sortBed debian/bedtools/usr/bin/
cp -a ./bin/subtractBed debian/bedtools/usr/bin/
cp -a ./bin/tagBam debian/bedtools/usr/bin/
cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
cp -a ./bin/windowBed debian/bedtools/usr/bin/
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
install -d debian/bedtools/etc/bash_completion.d
cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
cd debian/bedtools
chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
cd '/«PKGBUILDDIR»'
dh_fixperms -pbedtools
find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/bedtools -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/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
rm -f debian/bedtools/DEBIAN/shlibs
rm /«PKGBUILDDIR»/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
find debian/bedtools/etc -type f -printf '/etc/%P
' >> debian/bedtools/DEBIAN/conffiles
chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
echo misc:Depends= >> debian/bedtools.substvars
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/bedtools/DEBIAN/control
chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
(cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/bedtools/DEBIAN/md5sums
chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
dpkg-deb -Z xz --build debian/bedtools ..
dpkg-deb: building package `bedtools' in `../bedtools_2.19.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedtools_2.19.1-1_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 bedtools-2.19.1
dpkg-source: info: using options from bedtools-2.19.1/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140331-0551
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.19.1-1_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Fri, 21 Mar 2014 14:51:44 +0900
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.19.1-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
Changes:
bedtools (2.19.1-1) unstable; urgency=medium
.
479e63b Merge tag 'v2.19.1' into debian/unstable
.
[ Charles Plessy ]
93a7cf1 Create autopkgtest testsuite and a new package bedtools-test.
46183f8 debian/copyright: update path, correct license short name.
4fd441a debian/rules: removed obsolete exception of compression.
.
[ James McCoy ]
b4fa8e1 Move debian/upstream to debian/upstream/metadata
Checksums-Sha1:
e44d85677ae39a1fb9e3bd60d7785bdb1c938125 435380 bedtools_2.19.1-1_armhf.deb
Checksums-Sha256:
57ecda37ee1a5ef64f779203a8d4a8c762b05fbea9edbbc8de4598f343681012 435380 bedtools_2.19.1-1_armhf.deb
Files:
141605c53b91809c51a418fdcc868a23 435380 science optional bedtools_2.19.1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.19.1-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 435380 bytes: control archive=2128 bytes.
32 bytes, 1 lines conffiles
834 bytes, 18 lines control
2588 bytes, 45 lines md5sums
Package: bedtools
Version: 2.19.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1447
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
Description: suite of utilities for comparing genomic features
The BEDTools utilities allow one to address common genomics tasks such as
finding feature overlaps and computing coverage. The utilities are largely
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
.
The groupBy utility is distributed in the filo package.
drwxr-xr-x root/root 0 2014-03-31 05:50 ./
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/share/
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3288 2014-03-06 19:20 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 5339 2014-03-21 05:50 ./usr/share/doc/bedtools/copyright
-rw-r--r-- root/root 1542 2014-03-21 05:52 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 14454 2014-03-06 19:20 ./usr/share/doc/bedtools/changelog.gz
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2014-03-06 19:20 ./usr/share/bedtools/genomes/
-rwxr-xr-x root/root 856 2014-03-06 19:20 ./usr/share/bedtools/genomes/human.hg18.genome
-rwxr-xr-x root/root 1972 2014-03-06 19:20 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 1607 2014-03-06 19:20 ./usr/share/bedtools/genomes/mouse.mm10.genome.txt
-rwxr-xr-x root/root 565 2014-03-06 19:20 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rwxr-xr-x root/root 585 2014-03-06 19:20 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2014-03-31 05:50 ./usr/bin/
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2014-03-31 05:50 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2014-03-31 05:50 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 43 2014-03-31 05:50 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2014-03-31 05:50 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 40 2014-03-31 05:50 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2014-03-31 05:50 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2014-03-31 05:50 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2014-03-31 05:50 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2014-03-31 05:50 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2014-03-31 05:50 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2014-03-31 05:50 ./usr/bin/getOverlap
-rwxr-xr-x root/root 42 2014-03-31 05:50 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2014-03-31 05:50 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2014-03-31 05:50 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2014-03-31 05:50 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2014-03-31 05:50 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2014-03-31 05:50 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2014-03-31 05:50 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2014-03-31 05:50 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2014-03-31 05:50 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2014-03-31 05:50 ./usr/bin/randomBed
-rwxr-xr-x root/root 40 2014-03-31 05:50 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2014-03-31 05:50 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2014-03-31 05:50 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2014-03-31 05:50 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2014-03-31 05:50 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2014-03-31 05:50 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2014-03-31 05:50 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2014-03-31 05:50 ./usr/bin/windowMaker
-rwxr-xr-x root/root 1448208 2014-03-31 05:50 ./usr/bin/bedtools
drwxr-xr-x root/root 0 2014-03-31 05:50 ./etc/
drwxr-xr-x root/root 0 2014-03-31 05:50 ./etc/bash_completion.d/
-rw-r--r-- root/root 638 2014-03-21 04:17 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 103044
Build-Time: 1403
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 169
Job: bedtools_2.19.1-1
Machine Architecture: armhf
Package: bedtools
Package-Time: 1635
Source-Version: 2.19.1-1
Space: 103044
Status: successful
Version: 2.19.1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140331-0551
Build needed 00:27:15, 103044k disc space