Raspbian Package Auto-Building

Build log for bedtools (2.20.1-1) on armhf

bedtools2.20.1-1armhf → 2014-07-25 05:45:46

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01

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║ 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
Fetched 15.8 MB in 28s (548 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ 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]
Fetched 4228 kB in 0s (4339 kB/s)
Download complete and in download only mode

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-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.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
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
Fetched 13.9 MB in 3s (4179 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11827 files and directories currently installed.)
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Unpacking libpipeline1:armhf (1.3.0-1) ...
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Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
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) ...
Setting up python2.7 (2.7.8-1) ...
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
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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