bedtools →
2.20.1-1 →
armhf → 2014-07-25 05:45:46
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ bedtools 2.20.1-1 (armhf) 25 Jul 2014 05:20 ║
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Package: bedtools
Version: 2.20.1-1
Source Version: 2.20.1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bedtools-qRqqAO/bedtools-2.20.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bedtools-qRqqAO' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-e09b5cc9-d8a0-4f38-b00f-7c546a191c44' 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 [7421 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8407 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 4228 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main bedtools 2.20.1-1 (dsc) [2072 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main bedtools 2.20.1-1 (tar) [4219 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bedtools 2.20.1-1 (diff) [6524 B]
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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-t8kUIY/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 38 not upgraded.
Need to get 0 B/814 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 ... 11827 files and directories currently installed.)
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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), debhelper (>= 9), python, zlib1g-dev, samtools
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), python, zlib1g-dev, samtools
dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-h9FIKl/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 debhelper 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 samtools
zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
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 debhelper 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 samtools
sbuild-build-depends-bedtools-dummy zlib1g-dev
0 upgraded, 31 newly installed, 0 to remove and 38 not upgraded.
Need to get 13.9 MB/13.9 MB of archives.
After this operation, 42.9 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1h-3 [830 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-6 [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 2.6.7.1-1 [964 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-4 [29.4 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.19-1 [232 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.8.5-2 [357 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-4 [698 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.8-1 [347 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.8-1 [1110 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 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 2.1.0-6 [60.2 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 1:5.19-1 [57.7 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-4 [111 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.56 [35.5 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.8-1 [1834 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.8-1 [243 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.8-1 [39.8 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.8-1 [19.2 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.8-1 [150 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-4 [1134 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main samtools armhf 0.1.19-1 [523 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.3.0-1) ...
Setting up libssl1.0.0:armhf (1.0.1h-3) ...
Setting up groff-base (1.22.2-6) ...
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 (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-4) ...
Setting up libmagic1:armhf (1:5.19-1) ...
Setting up libsqlite3-0:armhf (3.8.5-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-4) ...
Setting up libpython2.7-minimal:armhf (2.7.8-1) ...
Setting up python2.7-minimal (2.7.8-1) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.40.0-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libexpat1:armhf (2.1.0-6) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up file (1:5.19-1) ...
Setting up gettext-base (0.18.3.2-4) ...
Setting up mime-support (3.56) ...
Setting up libpython2.7-stdlib:armhf (2.7.8-1) ...
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Setting up python-minimal (2.7.8-1) ...
Setting up libpython-stdlib:armhf (2.7.8-1) ...
Setting up python (2.7.8-1) ...
Setting up gettext (0.18.3.2-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20140613) ...
Setting up samtools (0.1.19-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-7) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.15-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140617-1 dpkg-dev_1.17.10 g++-4.9_4.9.0-7 gcc-4.8_4.8.3-4 gcc-4.9_4.9.0-7 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.6 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140617-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-4 cpp-4.8_4.8.3-4 cpp-4.9_4.9.0-7 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1.1 e2fsprogs_1.42.10-1.1 fakeroot_1.18.4-2 file_1:5.19-1 findutils_4.4.2-9 g++_4:4.9.0-4 g++-4.9_4.9.0-7 gcc_4:4.9.0-4 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-4 gcc-4.8-base_4.8.3-4 gcc-4.9_4.9.0-7 gcc-4.9-base_4.9.0-7 gettext_0.18.3.2-4 gettext-base_0.18.3.2-4 gnupg_1.4.18-2 gpgv_1.4.18-2 grep_2.18-2 groff-base_1.22.2-6 gzip_1.6-3 hostname_3.15 init-system-helpers_1.19 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.6 libasan0_4.8.3-4 libasan1_4.9.0-7 libasprintf0c2_0.18.3.2-4 libatomic1_4.9.0-7 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-7 libc-dev-bin_2.19-7 libc6_2.19-7 libc6-dev_2.19-7 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-5 libdbus-1-3_1.8.6-1 libdpkg-perl_1.17.10 libexpat1_2.1.0-6 libffi6_3.1-2 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-4 libgcc-4.9-dev_4.9.0-7 libgcc1_1:4.9.0-7 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.0-7 libisl10_0.12.2-2 libklibc_2.0.3-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-8 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmount1_2.20.1-5.8 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-1 libpython2.7-stdlib_2.7.8-1 libreadline6_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-17 libsqlite3-0_3.8.5-2 libss2_1.42.10-1.1 libssl1.0.0_1.0.1h-3 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libubsan0_4.9.0-7 libudev1_204-14 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mime-support_3.56 mount_2.20.1-5.8 multiarch-support_2.19-7 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-6 perl-base_5.18.2-6 perl-modules_5.18.2-6 plymouth_0.9.0-4 po-debconf_1.0.16+nmu3 procps_1:3.3.9-5 python_2.7.8-1 python-minimal_2.7.8-1 python2.7_2.7.8-1 python2.7-minimal_2.7.8-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 samtools_0.1.19-1 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 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 udev_204-14 util-linux_2.20.1-5.8 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jun 6 20:10:34 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bedtools_2.20.1-1.dsc
dpkg-source: info: extracting bedtools in bedtools-2.20.1
dpkg-source: info: unpacking bedtools_2.20.1.orig.tar.gz
dpkg-source: info: unpacking bedtools_2.20.1-1.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-e09b5cc9-d8a0-4f38-b00f-7c546a191c44
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 2.20.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build bedtools-2.20.1
dpkg-buildpackage: host architecture armhf
dpkg-source: info: using options from bedtools-2.20.1/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 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
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.20.1
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
* compiling ContextMerge.cpp
* compiling ContextJaccard.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 EmptyRecord.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 StrandQueue.cpp
* compiling FileRecordMgr.cpp
* compiling FileRecordMergeMgr.cpp
- Building in src/utils/general
* compiling QuickString.cpp
* compiling ParseTools.cpp
* compiling PushBackStreamBuf.cpp
* compiling CompressionTools.cpp
* compiling Tokenizer.cpp
- Building in src/utils/gzstream
g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -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/mergeFile
* compiling mergeMain.cpp
* compiling mergeFile.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»'
dh_auto_test -a
make -j1 test
make[1]: Entering directory '/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.20.1
CURRENT_VERSION = v2.20.1
* Creating BamTools API
- Building in src/utils/bedFile
make[2]: '../../../obj//bedFile.o' is up to date.
- Building in src/utils/BinTree
make[2]: '../../../obj//BinTree.o' is up to date.
- Building in src/utils/version
make[2]: Nothing to be done for 'all'.
- Building in src/utils/bedGraphFile
make[2]: '../../../obj//bedGraphFile.o' is up to date.
- Building in src/utils/chromsweep
make[2]: '../../../obj//chromsweep.o' is up to date.
- Building in src/utils/Contexts
make[2]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools
- Building in FileReaders
make[3]: Nothing to be done for 'all'.
- Building in Records
make[3]: Nothing to be done for 'all'.
* compiling FileRecordMgr.cpp
* compiling FileRecordMergeMgr.cpp
- Building in src/utils/general
make[2]: Nothing to be done for 'all'.
- Building in src/utils/gzstream
make[2]: '../../../obj//gzstream.o' is up to date.
- Building in src/utils/fileType
make[2]: Nothing to be done for 'all'.
- Building in src/utils/bedFilePE
make[2]: '../../../obj//bedFilePE.o' is up to date.
- Building in src/utils/KeyListOps
make[2]: Nothing to be done for 'all'.
- Building in src/utils/NewChromsweep
make[2]: '../../../obj//NewChromsweep.o' is up to date.
- Building in src/utils/sequenceUtilities
make[2]: '../../../obj//sequenceUtils.o' is up to date.
- Building in src/utils/tabFile
make[2]: '../../../obj//tabFile.o' is up to date.
- Building in src/utils/BamTools
make[2]: Nothing to be done for 'all'.
- Building in src/utils/BamTools-Ancillary
make[2]: Nothing to be done for 'all'.
- Building in src/utils/BlockedIntervals
make[2]: Nothing to be done for 'all'.
- Building in src/utils/Fasta
make[2]: Nothing to be done for 'all'.
- Building in src/utils/VectorOps
make[2]: '../../../obj//VectorOps.o' is up to date.
- Building in src/utils/GenomeFile
make[2]: '../../../obj//NewGenomeFile.o' is up to date.
- Building in src/utils/RecordOutputMgr
make[2]: '../../../obj//RecordOutputMgr.o' is up to date.
- Building in src/annotateBed
make[2]: Nothing to be done for 'all'.
- Building in src/bamToBed
make[2]: Nothing to be done for 'all'.
- Building in src/bamToFastq
make[2]: Nothing to be done for 'all'.
- Building in src/bedToBam
make[2]: Nothing to be done for 'all'.
- Building in src/bedpeToBam
make[2]: Nothing to be done for 'all'.
- Building in src/bedToIgv
make[2]: Nothing to be done for 'all'.
- Building in src/bed12ToBed6
make[2]: Nothing to be done for 'all'.
- Building in src/closestBed
make[2]: Nothing to be done for 'all'.
- Building in src/clusterBed
make[2]: Nothing to be done for 'all'.
- Building in src/complementBed
make[2]: Nothing to be done for 'all'.
- Building in src/coverageBed
make[2]: Nothing to be done for 'all'.
- Building in src/expand
make[2]: Nothing to be done for 'all'.
- Building in src/fastaFromBed
make[2]: Nothing to be done for 'all'.
- Building in src/flankBed
make[2]: Nothing to be done for 'all'.
- Building in src/genomeCoverageBed
make[2]: Nothing to be done for 'all'.
- Building in src/getOverlap
make[2]: Nothing to be done for 'all'.
- Building in src/groupBy
make[2]: Nothing to be done for 'all'.
- Building in src/intersectFile
make[2]: Nothing to be done for 'all'.
- Building in src/jaccard
make[2]: Nothing to be done for 'all'.
- Building in src/linksBed
make[2]: Nothing to be done for 'all'.
- Building in src/maskFastaFromBed
make[2]: Nothing to be done for 'all'.
- Building in src/mapFile
make[2]: Nothing to be done for 'all'.
- Building in src/mergeFile
make[2]: Nothing to be done for 'all'.
- Building in src/multiBamCov
make[2]: Nothing to be done for 'all'.
- Building in src/multiIntersectBed
make[2]: Nothing to be done for 'all'.
- Building in src/nekSandbox1
make[2]: Nothing to be done for 'all'.
- Building in src/nucBed
make[2]: Nothing to be done for 'all'.
- Building in src/pairToBed
make[2]: Nothing to be done for 'all'.
- Building in src/pairToPair
make[2]: Nothing to be done for 'all'.
- Building in src/randomBed
make[2]: Nothing to be done for 'all'.
- Building in src/regressTest
compiling RegressTest.cpp
compiling regressTestMain.cpp
- Building in src/reldist
make[2]: Nothing to be done for 'all'.
- Building in src/sampleFile
make[2]: Nothing to be done for 'all'.
- Building in src/shuffleBed
make[2]: Nothing to be done for 'all'.
- Building in src/slopBed
make[2]: Nothing to be done for 'all'.
- Building in src/sortBed
make[2]: Nothing to be done for 'all'.
- Building in src/subtractBed
make[2]: Nothing to be done for 'all'.
- Building in src/tagBam
make[2]: Nothing to be done for 'all'.
- Building in src/unionBedGraphs
make[2]: Nothing to be done for 'all'.
- Building in src/windowBed
make[2]: Nothing to be done for 'all'.
- Building in src/windowMaker
make[2]: Nothing to be done for 'all'.
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
Performing general tests:
general.t01...\c
ok
general.t02...\c
ok
general.t03...\c
ok
general.t04...\c
ok
general.t05...\c
ok
general.t06...\c
ok
general.t07...\c
ok
general.t08...\c
ok
general.t09...\c
ok
general.t10...\c
ok
general.t11...\c
ok
general.t12...\c
ok
general.t13...\c
ok
general.t14...\c
ok
general.15...\c
ok
general.t16...\c
ok
general.t17...\c
ok
general.t18...\c
ok
general.t19...\c
ok
general.t20...\c
ok
general.t21...\c
ok
general.22...\c
ok
general.t23...\c
ok
general.t24...\c
ok
general.t25...\c
ok
general.t26...\c
ok
general.t27...\c
ok
general.t28...\c
ok
general.29...\c
ok
general.t30...\c
ok
general.t31...\c
ok
general.t32...\c
ok
general.t33...\c
ok
general.t34...\c
ok
general.t35...\c
ok
general.36...\c
ok
general.t37...\c
ok
general.t38...\c
ok
general.t39...\c
ok
general.t40...\c
ok
general.t41...\c
ok
general.t42...\c
ok
Testing bedtools bed12tobed6:
bed12tobed6.t1...\c
ok
bed12tobed6.t2...\c
ok
bed12tobed6.t3...\c
ok
bed12tobed6.t4...\c
ok
bed12tobed6.t5...\c
ok
Testing bedtools bamtobed:
bamtobed.t1...\c
ok
bamtobed.t2...\c
ok
bamtobed.t3...\c
ok
bamtobed.t4...\c
ok
bamtobed.t5...\c
ok
bamtobed.t6...\c
ok
bamtobed.t7...\c
ok
bamtobed.t8...\c
ok
bamtobed.t9...\c
ok
bamtobed.t10...\c
ok
bamtobed.t9...\c
ok
bamtobed.t11...\c
ok
Testing bedtools closest:
closest.t1...\c
ok
closest.t2...\c
ok
closest.t3...\c
ok
closest.t4...\c
ok
closest.t5...\c
ok
closest.t6...\c
ok
closest.t7...\c
ok
closest.t8...\c
ok
closest.t9...\c
ok
closest.t10...\c
ok
closest.t11...\c
ok
closest.t12...\c
ok
Testing bedtools cluster:
cluster.t1...\c
ok
cluster.t2...\c
ok
Testing bedtools coverage:
Testing bedtools expand:
expand.t1...\c
ok
expand.t2...\c
ok
expand.t3...\c
ok
Testing bedtools flank:
flank.t1...\c
ok
flank.t2...\c
ok
flank.t3...\c
ok
flank.t4...\c
ok
flank.t5...\c
ok
flank.t6...\c
ok
flank.t7...\c
ok
flank.t8...\c
ok
flank.t9...\c
ok
flank.t10...\c
ok
flank.t11...\c
ok
Testing bedtools genomecov:
genomecov.t1...\c
ok
genomecov.t2...\c
ok
genomecov.t3...\c
ok
genomecov.t4...\c
ok
genomecov.t5...\c
ok
genomecov.t6...\c
ok
genomecov.t7...\c
ok
Testing bedtools getfasta:
getfasta.t01...\c
ok
getfasta.t02...\c
ok
getfasta.t03...\c
ok
getfasta.t04...\c
ok
getfasta.t05...\c
ok
getfasta.t06...\c
ok
getfasta.t07...\c
ok
Testing bedtools intersect:
intersect.t01...\c
ok
intersect.t02...\c
ok
intersect.t03...\c
ok
intersect.t04...\c
ok
intersect.t05...\c
ok
intersect.t06...\c
ok
intersect.t07...\c
ok
intersect.t08...\c
ok
intersect.t09...\c
ok
intersect.t10...\c
ok
intersect.t11...\c
ok
intersect.t12...\c
ok
intersect.t13...\c
ok
intersect.t14...\c
ok
intersect.t15...\c
ok
intersect.t16...\c
ok
intersect.t17...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t18...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t19...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t20...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t21...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t22...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t22.a...\c
ok
intersect.t22.b...\c
ok
intersect.t22.c...\c
ok
intersect.t22.d...\c
ok
intersect.t22.e...\c
ok
intersect.t22.f...\c
ok
intersect.t23...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t24...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
ok
intersect.t25...\c
ok
intersect.t26...\c
ok
intersect.t27...\c
ok
intersect.t28...\c
ok
intersect.t29...\c
ok
intersect.t30...\c
ok
intersect.t31...\c
ok
intersect.t32...\c
ok
intersect.t33...\c
ok
intersect.t34...\c
ok
intersect.t35...\c
ok
intersect.t36...\c
ok
intersect.t37...\c
intersect.new.t01...\c
ok
intersect.new.t02...\c
ok
intersect.new.t03...\c
ok
intersect.new.t04...\c
ok
intersect.new.t05...\c
ok
intersect.new.t06...\c
ok
intersect.new.t07...\c
ok
intersect.new.t08...\c
ok
intersect.new.t09...\c
ok
intersect.new.t10...\c
ok
intersect.new.t11...\c
ok
intersect.new.t12...\c
ok
intersect.new.t13...\c
ok
intersect.new.t14...\c
ok
intersect.new.t15...\c
ok
intersect.new.t16...\c
ok
intersect.new.t17...\c
ok
intersect.new.t18...\c
ok
intersect.new.t19...\c
ok
intersect.new.t20...\c
ok
intersect.new.t20.b...\c
ok
intersect.new.t20.c...\c
ok
intersect.new.t21...\c
ok
intersect.new.t22...\c
ok
intersect.new.t23...\c
ok
intersect.new.t24...\c
ok
intersect.new.t25...\c
ok
intersect.new.t26...\c
ok
intersect.new.t27...\c
ok
intersect.new.t28...\c
ok
intersect.new.t29...\c
ok
intersect.new.t30...\c
ok
intersect.new.t31...\c
ok
intersect.new.t32...\c
ok
intersect.new.t33...\c
ok
intersect.new.t34...\c
ok
intersect.new.t35...\c
ok
intersect.new.t36...\c
ok
intersect.new.t37...\c
ok
intersect.new.t38...\c
ok
intersect.new.t39...\c
ok
intersect.new.t40...\c
ok
intersect.new.t41...\c
ok
intersect.new.t42...\c
ok
intersect.new.t43...\c
ok
intersect.new.t44...\c
ok
intersect.new.t45...\c
ok
intersect.new.t46...\c
ok
intersect.new.t47...\c
ok
intersect.new.t48...\c
ok
intersect.new.t49...\c
ok
intersect.new.t50...\c
ok
intersect.new.t51...\c
ok
intersect.new.t52...\c
ok
intersect.new.t53...\c
ok
intersect.new.t54...\c
ok
intersect.new.t55...\c
ok
intersect.new.t56...\c
ok
intersect.new.t57...\c
ok
intersect.new.t58...\c
ok
intersect.new.t59...\c
ok
intersect.new.t60...\c
ok
intersect.new.t61...\c
new_test-intersect.sh: line 728: bgzip: command not found
Error: Unable to open file dummy.txt.gz. Exiting.
0a1
> #Random Header
fail
rm: cannot remove 'dummy.txt.gz': No such file or directory
intersect.new.t62...\c
ok
intersect.new.t63...\c
ok
intersect.new.t64...\c
ok
Testing bedtools jaccard:
jaccard.t01...\c
ok
jaccard.t02...\c
ok
jaccard.t03...\c
ok
jaccard.t04...\c
ok
jaccard.t05...\c
ok
jaccard.t06...\c
ok
jaccard.t07...\c
ok
jaccard.t08...\c
ok
jaccard.t09...\c
ok
jaccard.t10...\c
ok
jaccard.t11...\c
ok
jaccard.t12...\c
ok
jaccard.t13...\c
ok
Testing bedtools map:
map.t01...\c
ok
map.t02...\c
ok
map.t03...\c
ok
map.t04...\c
ok
map.t05...\c
ok
map.t06...\c
ok
map.t07...\c
ok
map.t08...\c
ok
map.t09...\c
ok
map.t10...\c
ok
map.t11...\c
ok
map.t12...\c
ok
map.t13...\c
ok
map.t14...\c
ok
map.t15...\c
ok
map.t16...\c
ok
map.t17...\c
ok
map.t18...\c
ok
map.t19...\c
ok
map.t20...\c
ok
map.t21...\c
ok
map.t22..\c
ok
map.t23..\c
ok
map.t24..\c
ok
map.t25..\c
ok
map.t26..\c
ok
map.t27..\c
ok
map.t28..\c
ok
map.t29..\c
ok
map.t30..\c
ok
map.t31..\c
ok
map.t32..\c
ok
map.t33..\c
ok
map.t33..\c
ok
map.t33..\c
ok
map.t34..\c
ok
map.t35..\c
ok
map.t36..\c
ok
map.t37..\c
ok
map.t38..\c
ok
map.t39..\c
ok
map.t40..\c
ok
map.t41..\c
ok
map.t42..\c
ok
map.t43..\c
ok
map.t44...\c
ok
map.t45...\c
ok
map.t46...\c
ok
map.t47...\c
ok
map.t48...\c
ok
map.t49...\c
ok
map.t50...\c
ok
map.t51...\c
ok
map.t52...\c
ok
map.t53...\c
ok
Testing bedtools merge:
merge.t1...\c
ok
merge.t2...\c
ok
merge.t3...\c
ok
merge.t4...\c
ok
merge.t5...\c
ok
merge.t6...\c
ok
merge.t7...\c
ok
merge.t8...\c
ok
merge.t9...\c
ok
merge.t10...\c
ok
merge.t11...\c
ok
merge.t12...\c
ok
merge.t13...\c
ok
merge.t14...\c
ok
merge.t15...\c
ok
merge.t16...\c
ok
merge.t17...\c
ok
merge.t18...\c
ok
merge.t19...\c
ok
merge.t20...\c
ok
merge.t21...\c
ok
merge.t22...\c
ok
merge.t23a...\c
ok
merge.t23b...\c
ok
merge.t24...\c
ok
merge.t25...\c
ok
merge.t26...\c
ok
merge.t27...\c
ok
merge.t28...\c
ok
merge.t29...\c
ok
merge.t30...\c
ok
merge.t31...\c
ok
merge.t32...\c
ok
merge.t33...\c
ok
merge.t34...\c
ok
merge.t35...\c
ok
merge.t36...\c
ok
Testing bedtools multicov:
multicov.t1...\c
ok
multicov.t2...\c
ok
multicov.t3...\c
ok
multicov.t4...\c
ok
multicov.t5...\c
ok
multicov.t6...\c
ok
multicov.t7...\c
ok
multicov.t8...\c
ok
multicov.t9...\c
ok
Testing bedtools reldist:
reldist.t01...\c
2c2
< 0.00 43423 43423 1.000
---
> 0.00 43424 43424 1.000
fail
reldist.t02...\c
ok
reldist.t03...\c
ok
Testing bedtools slop:
slop.t1...\c
ok
slop.t2...\c
ok
slop.t3...\c
ok
slop.t4...\c
ok
slop.t5...\c
ok
slop.t6...\c
ok
slop.t7...\c
ok
slop.t8...\c
ok
slop.t9...\c
ok
slop.t10...\c
ok
slop.t11...\c
ok
slop.t12...\c
ok
slop.t13...\c
ok
slop.t14...\c
ok
Testing bedtools shuffle:
shuffle.t1...\c
1,10c1,10
< chr4 18120316 18120784 trf 789
< chr21 7219372 7219545 trf 346
< chr3 44696764 44697004 trf 434
< chr4 174464900 174465122 trf 273
< chr12 94822425 94822602 trf 187
< chr8 95576893 95577058 trf 199
< chr14 83751413 83751551 trf 242
< chr8 85463512 85463547 trf 70
< chr6 120627488 120627585 trf 79
< chr8 48095009 48095050 trf 73
---
> chr9 108600879 108601347 trf 789
> chr12 9186177 9186350 trf 346
> chr8 89726287 89726527 trf 434
> chr8 40323278 40323500 trf 273
> chr8 69904335 69904512 trf 187
> chr5 138240459 138240624 trf 199
> chr11 96382483 96382621 trf 242
> chr8 105834146 105834181 trf 70
> chrX 105921488 105921585 trf 79
> chrX 125331456 125331497 trf 73
fail
shuffle.t2...\c
1,20c1,20
< chr3 592740 593208 trf 789
< chr5 283241 283414 trf 346
< chr1 1146758 1146998 trf 434
< chr1 1614940 1615162 trf 273
< chr1 2523743 2523920 trf 187
< chr3 643143 643308 trf 199
< chr1 474504 474642 trf 242
< chr3 529762 529797 trf 70
< chr4 169448 169545 trf 79
< chr3 161259 161300 trf 73
< chr1 3976352 3976384 trf 64
< chr5 801033 801138 trf 149
< chr3 349579 349617 trf 58
< chr3 496504 496974 trf 278
< chr1 2520176 2520646 trf 339
< chr5 548307 548735 trf 202
< chr1 2185314 2185357 trf 59
< chr3 580280 580320 trf 62
< chr3 346921 346956 trf 52
< chr5 648960 649137 trf 302
---
> chr3 542223 542691 trf 789
> chr5 444343 444516 trf 346
> chr1 2520601 2520841 trf 434
> chr5 194760 194982 trf 273
> chr1 2121545 2121722 trf 187
> chr1 2246343 2246508 trf 199
> chr1 2724117 2724255 trf 242
> chr4 304892 304927 trf 70
> chr2 332618 332715 trf 79
> chr5 822410 822451 trf 73
> chr1 1450982 1451014 trf 64
> chr1 3218361 3218466 trf 149
> chr4 338952 338990 trf 58
> chr3 713207 713677 trf 278
> chr1 4378307 4378777 trf 339
> chr1 4451988 4452416 trf 202
> chr1 1545567 1545610 trf 59
> chr1 573175 573215 trf 62
> chr4 931201 931236 trf 52
> chr1 4215777 4215954 trf 302
fail
shuffle.t3...\c
1,20c1,20
< chr2 128881 129349 trf 789
< chr2 146758 146931 trf 346
< chr2 800535 800775 trf 434
< chr4 643143 643365 trf 273
< chr3 233696 233873 trf 187
< chr3 169448 169613 trf 199
< chr4 313867 314005 trf 242
< chr3 801033 801068 trf 70
< chr3 541169 541266 trf 79
< chr5 520176 520217 trf 73
< chr4 112916 112948 trf 64
< chr5 580280 580385 trf 149
< chr5 195221 195259 trf 58
< chr1 527447 527917 trf 278
< chr1 4001951 4002421 trf 339
< chr2 391843 392271 trf 202
< chr1 2069454 2069497 trf 59
< chr5 877263 877303 trf 62
< chr5 743195 743230 trf 52
< chr1 3931688 3931865 trf 302
---
> chr5 310009 310477 trf 789
> chr4 520601 520774 trf 346
> chr2 130650 130890 trf 434
> chr1 3246343 3246565 trf 273
> chr2 968160 968337 trf 187
> chr3 332618 332783 trf 199
> chr4 638727 638865 trf 242
> chr3 218361 218396 trf 70
> chr1 2259217 2259314 trf 79
> chr3 378307 378348 trf 73
> chr4 447387 447419 trf 64
> chr3 573175 573280 trf 149
> chr2 106791 106829 trf 58
> chr3 618697 619167 trf 278
> chr2 211901 212371 trf 339
> chr5 656883 657311 trf 202
> chr2 993338 993381 trf 59
> chr2 713531 713571 trf 62
> chr2 428268 428303 trf 52
> chr4 590632 590809 trf 302
fail
shuffle.t4...\c
ok
shuffle.t5...\c
1,10c1,10
< chr4 18120316 18120784 trf 789
< chr3 44696764 44697004 trf 434
< chr1 124123417 124123522 trf 149
< chr1 124123417 124123522 trf 149
< chr1 202671963 202672001 trf 58
< chr1 202671963 202672001 trf 58
< chr2 14591939 14592409 trf 339
< chr2 8329659 8329699 trf 62
< chr1 120971344 120971521 trf 302
< chr1 120971344 120971521 trf 302
---
> chr1 150415830 150415862 trf 64
> chr1 150415830 150415862 trf 64
> chr5 78078743 78079213 trf 339
> chr4 84711820 84712248 trf 202
> chr4 61777751 61777794 trf 59
> chr3 28583223 28583400 trf 302
> chr1 55933709 55934092 trf 712
> chr1 55933709 55934092 trf 712
> chr1 39686691 39686725 trf 68
> chr2 2555287 2555330 trf 86
fail
Testing bedtools subtract:
subtract.t1...\c
ok
subtract.t2...\c
ok
subtract.t3...\c
ok
subtract.t4...\c
ok
subtract.t5...\c
ok
subtract.t6...\c
ok
subtract.t7...\c
ok
subtract.t8...\c
ok
subtract.t9...\c
ok
subtract.t10...\c
ok
Testing bedtools sample:
sample.t01...\c
ok
sample.new.t02...\c
ok
sample.new.t03...\c
ok
sample.new.t04...\c
ok
sample.new.t05...\c
ok
sample.new.t06...\c
ok
sample.new.t07...\c
ok
sample.new.t08...\c
ok
sample.new.t09...\c
ok
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
rm -rf debian/bedtools/
dh_auto_install -a
install -d debian/bedtools
debian/rules override_dh_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_install
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/
rm -f /«PKGBUILDDIR»/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installdocs -a
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
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_installchangelogs 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
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_perl -a
dh_link -a
dh_compress -a
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»'
debian/rules override_dh_fixperms
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_fixperms
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
chmod -x /«PKGBUILDDIR»/debian/bedtools/usr/share/bedtools/genomes/*.genome
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_strip -a
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_makeshlibs -a
rm -f debian/bedtools/DEBIAN/shlibs
dh_shlibdeps -a
install -o 0 -g 0 -d debian/bedtools/DEBIAN
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
find debian/bedtools/etc -type f -printf '/etc/%P
' >> debian/bedtools/DEBIAN/conffiles
chmod 644 debian/bedtools/DEBIAN/conffiles
dh_gencontrol -a
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 -a
(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 -a
dpkg-deb --build debian/bedtools ..
dpkg-deb: building package `bedtools' in `../bedtools_2.20.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedtools_2.20.1-1_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-2.20.1
dpkg-source: info: using options from bedtools-2.20.1/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140725-0545
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.20.1-1_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Fri, 06 Jun 2014 21:50:39 +0200
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.20.1-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
Changes:
bedtools (2.20.1-1) unstable; urgency=medium
.
* New upstream version
* Fix permission of some genome example files
Checksums-Sha1:
8b1aff05b8735a77ec575ca10f2d77dc0f3a97ac 478854 bedtools_2.20.1-1_armhf.deb
Checksums-Sha256:
4ee82ef2b0a102a38467be6ea80ad2f3047d8a8249a949d80895419c77f13d62 478854 bedtools_2.20.1-1_armhf.deb
Files:
52c0c9af5adbb030fd17ca8bff3b6200 478854 science optional bedtools_2.20.1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.20.1-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 478854 bytes: control archive=2130 bytes.
32 bytes, 1 lines conffiles
836 bytes, 18 lines control
2588 bytes, 45 lines md5sums
Package: bedtools
Version: 2.20.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1705
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.9), zlib1g (>= 1:1.2.3.3)
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 2014-07-25 05:44 ./
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/bin/
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2014-07-25 05:43 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2014-07-25 05:43 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 43 2014-07-25 05:43 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2014-07-25 05:43 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 40 2014-07-25 05:43 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2014-07-25 05:43 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2014-07-25 05:43 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2014-07-25 05:43 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2014-07-25 05:43 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2014-07-25 05:43 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2014-07-25 05:43 ./usr/bin/getOverlap
-rwxr-xr-x root/root 42 2014-07-25 05:43 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2014-07-25 05:43 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2014-07-25 05:43 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2014-07-25 05:43 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2014-07-25 05:43 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2014-07-25 05:43 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2014-07-25 05:43 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2014-07-25 05:43 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2014-07-25 05:43 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2014-07-25 05:43 ./usr/bin/randomBed
-rwxr-xr-x root/root 40 2014-07-25 05:43 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2014-07-25 05:43 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2014-07-25 05:43 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2014-07-25 05:43 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2014-07-25 05:43 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2014-07-25 05:43 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2014-07-25 05:43 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2014-07-25 05:43 ./usr/bin/windowMaker
-rwxr-xr-x root/root 1710984 2014-07-25 05:44 ./usr/bin/bedtools
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/share/
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2014-05-24 01:33 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 856 2014-05-24 01:33 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1972 2014-05-24 01:33 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 1607 2014-05-24 01:33 ./usr/share/bedtools/genomes/mouse.mm10.genome.txt
-rw-r--r-- root/root 565 2014-05-24 01:33 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 585 2014-05-24 01:33 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-07-25 05:44 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3346 2014-05-24 01:33 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 5339 2014-06-06 20:07 ./usr/share/doc/bedtools/copyright
-rw-r--r-- root/root 1764 2014-06-06 20:07 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 14752 2014-05-24 01:33 ./usr/share/doc/bedtools/changelog.gz
drwxr-xr-x root/root 0 2014-07-25 05:44 ./etc/
drwxr-xr-x root/root 0 2014-07-25 05:44 ./etc/bash_completion.d/
-rw-r--r-- root/root 638 2014-06-06 20:07 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 18800
Build-Time: 1234
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 183
Job: bedtools_2.20.1-1
Machine Architecture: armhf
Package: bedtools
Package-Time: 1470
Source-Version: 2.20.1-1
Space: 18800
Status: successful
Version: 2.20.1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140725-0545
Build needed 00:24:30, 18800k disc space