bedtools →
2.24.0-2 →
armhf → 2015-07-22 05:59:26
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ bedtools 2.24.0-2 (armhf) 22 Jul 2015 05:30 ║
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Package: bedtools
Version: 2.24.0-2
Source Version: 2.24.0-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bedtools-6kCQPi/bedtools-2.24.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bedtools-6kCQPi' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-c8d2b843-f419-4a22-8cba-45e30a2e8df9' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
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Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8120 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.0 MB]
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Building dependency tree...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/bedtools.git
Need to get 18.4 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main bedtools 2.24.0-2 (dsc) [2071 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main bedtools 2.24.0-2 (tar) [18.4 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bedtools 2.24.0-2 (diff) [9256 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-z4mwiA/apt_archive/sbuild-build-depends-core-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
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Installing build dependencies
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Building dependency tree...
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 84 not upgraded.
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, samtools
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, samtools
dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-Za2m3t/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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 xdg-user-dirs 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 84 not upgraded.
Need to get 14.3 MB/14.3 MB of archives.
After this operation, 44.6 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-3 [380 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-3 [1163 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.58 [36.0 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10.2-1 [389 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-3 [1815 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-3 [259 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main samtools armhf 0.1.19-1 [523 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
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Setting up libpipeline1:armhf (1.4.0-1) ...
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Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libexpat1_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-3 libpython2.7-stdlib_2.7.10-3 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libsqlite3-0_3.8.10.2-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 python_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-3 python2.7-minimal_2.7.10-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 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 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Jul 16 12:38:26 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bedtools_2.24.0-2.dsc
dpkg-source: info: extracting bedtools in bedtools-2.24.0
dpkg-source: info: unpacking bedtools_2.24.0.orig.tar.gz
dpkg-source: info: unpacking bedtools_2.24.0-2.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying fix_test_script.patch
dpkg-source: info: applying 0001-settle-on-uint32_t-signature-for-QuickString.-Resolv.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-c8d2b843-f419-4a22-8cba-45e30a2e8df9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
dpkg-buildpackage: source version 2.24.0-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build bedtools-2.24.0
dpkg-buildpackage: host architecture armhf
dpkg-source: info: using options from bedtools-2.24.0/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 -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -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 = v2.24.0
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 ContextFisher.cpp
* compiling ContextMap.cpp
* compiling ContextSample.cpp
* compiling ContextSpacing.cpp
* compiling ContextMerge.cpp
* compiling ContextJaccard.cpp
* compiling ContextClosest.cpp
* compiling ContextSubtract.cpp
* compiling ContextCoverage.cpp
- Building in src/utils/FileRecordTools
* compiling FileRecordMgr.cpp
* compiling FileRecordMergeMgr.cpp
- Building in FileReaders
* compiling FileReader.cpp
* compiling SingleLineDelimTextFileReader.cpp
* compiling BamFileReader.cpp
* compiling BufferedStreamMgr.cpp
* compiling InputStreamMgr.cpp
- Building in Records
* 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 BlockMgr.cpp
* compiling StrandQueue.cpp
* compiling RecordMgr.cpp
* compiling RecordList.cpp
* compiling RecordKeyList.cpp
* compiling RecordKeyVector.cpp
- Building in src/utils/FileRecordTools/FileReaders
make[2]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools/Records
make[2]: Nothing to be done for 'all'.
- Building in src/utils/general
* compiling QuickString.cpp
* compiling ParseTools.cpp
ParseTools.cpp: In function 'int str2chrPos(const char*, size_t)':
ParseTools.cpp:31:7: warning: unused variable 'hasExponent' [-Wunused-variable]
bool hasExponent = false;
^
* compiling PushBackStreamBuf.cpp
* compiling CompressionTools.cpp
* compiling Tokenizer.cpp
* compiling CommonHelp.cpp
- Building in src/utils/gzstream
g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/aux -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
* compiling CloseSweep.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
* 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/utils/ToolBase
* compiling ToolBase.cpp
- Building in src/utils/aux
* compiling BedtoolsDriver.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/closestFile
* compiling closestHelp.cpp
* compiling closestFile.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/coverageFile
* compiling coverageHelp.cpp
* compiling coverageFile.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:80:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
bool haveOps = true;
^
- Building in src/intersectFile
* compiling intersectHelp.cpp
* compiling intersectFile.cpp
- Building in src/fisher
* compiling fisherHelp.cpp
* compiling fisher.cpp
* compiling kfunc.cpp
- Building in src/jaccard
* compiling jaccardHelp.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 mapHelp.cpp
* compiling mapFile.cpp
- Building in src/mergeFile
* compiling mergeHelp.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 sampleHelp.cpp
* compiling sampleFile.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)':
slopBed.cpp:86:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (int)_leftSlop) <= chromSize )
^
slopBed.cpp:100:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (int)_rightSlop) <= chromSize )
^
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- Building in src/spacingFile
* compiling spacingHelp.cpp
* compiling spacingFile.cpp
- Building in src/split
* compiling splitBed.cpp
* compiling splitBedMain.cpp
- Building in src/subtractFile
* compiling subtractHelp.cpp
* compiling subtractFile.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
* 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 = v2.24.0
CURRENT_VERSION = v2.24.0
* 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'.
- Building in src/utils/FileRecordTools/FileReaders
make[2]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools/Records
make[2]: Nothing to be done for 'all'.
- 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]: Nothing to be done for 'all'.
- 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/utils/ToolBase
make[2]: '../../../obj//ToolBase.o' is up to date.
- Building in src/utils/aux
make[2]: Nothing to be done for 'all'.
- 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/closestFile
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/coverageFile
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/fisher
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/spacingFile
make[2]: Nothing to be done for 'all'.
- Building in src/split
make[2]: Nothing to be done for 'all'.
- Building in src/subtractFile
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.t13...\c
ok
closest.t14...\c
ok
closest.t15...\c
ok
closest.t16...\c
ok
closest.t17...\c
ok
closest.t18...\c
ok
closest.t19...\c
ok
closest.t20...\c
ok
closest.t21...\c
ok
closest.t22...\c
ok
closest.t23...\c
ok
closest.t24...\c
ok
closest.t25...\c
ok
closest.t26...\c
ok
closest.t27...\c
ok
closest.t28...\c
ok
closest.t29...\c
ok
closest.t30...\c
ok
closest.t31...\c
ok
closest.t32...\c
ok
closest.t33...\c
ok
closest.t34...\c
ok
closest.t35...\c
ok
closest.t36...\c
ok
closest.t37...\c
ok
closest.t38...\c
ok
closest.t39...\c
ok
closest.t40...\c
ok
closest.t41...\c
ok
closest.t42...\c
ok
closest.t43...\c
ok
closest.t44...\c
ok
closest.t45...\c
ok
closest.t46...\c
ok
closest.t47...\c
ok
closest.t48...\c
ok
closest.t49...\c
ok
closest.t50...\c
ok
closest.t51...\c
ok
closest.t52...\c
ok
closest.t53...\c
ok
closest.t54...\c
ok
closest.t55...\c
ok
closest.t56...\c
ok
closest.t57...\c
ok
closest.t58...\c
ok
closest.t59...\c
ok
###########################################################
#
# CHROMOSOME SORT ORDER AND NAMING CONVENTIONS
#
###########################################################
closest.t01...\c
ok
closest.t02...\c
ok
closest.t03...\c
ok
closest.t04...\c
ok
closest.t05...\c
ok
closest.t06...\c
ok
closest.t07...\c
ok
closest.t08...\c
ok
closest.t09...\c
ok
closest.t10...\c
ok
closest.t11...\c
ok
closest.t12...\c
ok
closest.t13...\c
ok
closest.t14...\c
ok
closest.t15...\c
ok
closest.t16...\c
ok
closest.t17...\c
ok
closest.t18...\c
ok
closest.t19...\c
ok
closest.20...\c
ok
closest.21...\c
ok
closest.22...\c
ok
closest.23...\c
ok
###########################################################
#
# K CLOSEST HITS TESTS
#
###########################################################
kclosest.t1...\c
ok
kclosest.t2...\c
ok
kclosest.t3...\c
ok
kclosest.t4...\c
ok
kclosest.t5...\c
ok
kclosest.t6...\c
ok
kclosest.t7...\c
ok
kclosest.t8...\c
ok
kclosest.t9...\c
ok
kclosest.t10...\c
ok
kclosest.t11...\c
ok
kclosest.t12...\c
ok
kclosest.t13...\c
ok
kclosest.t14...\c
ok
kclosest.t15...\c
ok
kclosest.t16...\c
ok
kclosest.t17...\c
ok
kclosest.t18...\c
ok
kclosest.t19...\c
ok
kclosest.t20...\c
ok
kclosest.t21...\c
ok
kclosest.t22...\c
ok
kclosest.t23...\c
ok
kclosest.t24...\c
ok
kclosest.t25...\c
ok
kclosest.t26...\c
ok
kclosest.t27...\c
ok
kclosest.t28...\c
ok
kclosest.t29...\c
ok
kclosest.t30...\c
ok
kclosest.t31...\c
ok
kclosest.t32...\c
ok
kclosest.t33...\c
ok
kclosest.t34...\c
ok
kclosest.t35...\c
ok
kclosest.t36...\c
ok
kclosest.t37...\c
ok
kclosest.t38...\c
ok
Testing bedtools cluster:
cluster.t1...\c
ok
cluster.t2...\c
ok
Testing bedtools coverage:
coverage.t1...\c
ok
coverage.t2...\c
ok
coverage.t3...\c
ok
coverage.t4...\c
ok
coverage.t5...\c
ok
coverage.t6...\c
ok
coverage.t7...\c
ok
coverage.t8...\c
ok
coverage.t9...\c
ok
coverage.t10...\c
ok
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 fisher:
fisher.t1...\c
ok
fisher.t2...\c
ok
fisher.t3...\c
ok
fisher.t4...\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
getfasta.t08...\c
index file test.iupac.fa.fai not found, generating...
ok
getfasta.t09...\c
index file test.iupac.fa.fai not found, generating...
ok
getfasta.t10...\c
index file test.fa.fai not found, generating...
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.t22.g...\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
ok
intersect.t38...\c
ok
intersect.t39...\c
ok
intersect.t40...\c
ok
intersect.t41...\c
ok
intersect.t42...\c
ok
intersect.t43...\c
ok
intersect.t44...\c
ok
intersect.t45...\c
ok
intersect.t46...\c
ok
intersect.t47...\c
ok
intersect.t48...\c
Error: Unable to open file bug223_d.vcf. Exiting.
1,4d0
< chr1 1 a G <DEL> 70.90
< chr1 1 a G <DEL> 70.90
< chr1 4 a G <DEL> 70.90
< chr1 4 a G <DEL> 70.90
fail
intersect.t49...\c
ok
intersect.t50...\c
ok
###########################################################
#
# MULTIPLE DATABASE INTERSECTION
#
###########################################################
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.t13...\c
ok
intersect.t14...\c
ok
intersect.t15...\c
ok
intersect.t16...\c
ok
intersect.t17...\c
ok
intersect.t18...\c
ok
intersect.t19...\c
ok
###########################################################
#
# CHROMOSOME SORT ORDER AND NAMING CONVENTIONS
#
###########################################################
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
ok
intersect.t18...\c
ok
intersect.t19...\c
ok
intersect.20...\c
ok
intersect.21...\c
ok
intersect.22...\c
ok
intersect.23...\c
ok
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 731: 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
intersect.new.t65...\c
ok
intersect.new.t66...\c
ok
intersect.new.t67...\c
ok
intersect.new.t68...\c
ok
Testing bedtools jaccard:
jaccard.t01...\c
ok
jaccard.t02...\c
ok
jaccard.t03...\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
merge.t37...\c
ok
merge.t38...\c
ok
merge.t39...\c
ok
merge.t40...\c
ok
merge.t41...\c
ok
merge.t42...\c
ok
merge.t43...\c
ok
merge.t44...\c
ok
merge.t45...\c
ok
merge.t46...\c
ok
merge.t47...\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
slop.t15...\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
subtract.t11...\c
ok
subtract.t12...\c
ok
subtract.t13...\c
ok
subtract.t14...\c
ok
subtract.t15...\c
ok
subtract.t16...\c
ok
subtract.t17...\c
ok
subtract.t18...\c
ok
subtract.t19...\c
ok
subtract.t20...\c
ok
subtract.t21...\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
Testing bedtools split:
slpit.size...\c
_tmp.00001.bed 10008118 201
_tmp.00002.bed 10008239 200
_tmp.00003.bed 10008196 200
_tmp.00004.bed 10008134 200
_tmp.00005.bed 10008211 200
_tmp.00006.bed 10008245 200
_tmp.00007.bed 10008130 200
_tmp.00008.bed 10008183 200
_tmp.00009.bed 10008140 200
_tmp.00010.bed 10008112 202
_tmp.00011.bed 10008115 201
_tmp.00012.bed 10008109 202
_tmp.00013.bed 10008118 200
_tmp.00014.bed 10008177 200
_tmp.00015.bed 10008186 200
_tmp.00016.bed 10008095 200
_tmp.00017.bed 10008244 200
_tmp.00018.bed 10008109 200
_tmp.00019.bed 10008186 200
_tmp.00020.bed 10008094 200
_tmp.00021.bed 10008089 200
_tmp.00022.bed 10008142 200
_tmp.00023.bed 10008075 200
_tmp.00024.bed 10008078 200
_tmp.00025.bed 10008102 201
_tmp.00026.bed 10008094 200
_tmp.00027.bed 10008267 200
_tmp.00028.bed 10008110 201
_tmp.00029.bed 10008106 200
_tmp.00030.bed 10008253 200
_tmp.00031.bed 10007982 200
_tmp.00032.bed 10007914 199
_tmp.00033.bed 10008248 200
_tmp.00034.bed 10008262 200
_tmp.00035.bed 10008130 200
_tmp.00036.bed 10008090 200
_tmp.00037.bed 10008135 200
_tmp.00038.bed 10007914 199
_tmp.00039.bed 10007947 199
_tmp.00040.bed 10008173 200
_tmp.00041.bed 10008158 200
_tmp.00042.bed 10007952 199
_tmp.00043.bed 10007973 199
_tmp.00044.bed 10007919 199
_tmp.00045.bed 10008243 200
_tmp.00046.bed 10007990 199
_tmp.00047.bed 10008101 200
_tmp.00048.bed 10008203 200
_tmp.00049.bed 10008177 200
_tmp.00050.bed 10007992 199
slpit.simple...\c
_tmp.00001.bed 10383293 200
_tmp.00002.bed 9689504 200
_tmp.00003.bed 9979394 200
_tmp.00004.bed 10044700 200
_tmp.00005.bed 10037664 200
_tmp.00006.bed 9927024 200
_tmp.00007.bed 9523076 200
_tmp.00008.bed 9755327 200
_tmp.00009.bed 10472367 200
_tmp.00010.bed 9957740 200
_tmp.00011.bed 9788244 200
_tmp.00012.bed 10206478 200
_tmp.00013.bed 9447400 200
_tmp.00014.bed 9929217 200
_tmp.00015.bed 9659419 200
_tmp.00016.bed 9680232 200
_tmp.00017.bed 9945910 200
_tmp.00018.bed 9120039 200
_tmp.00019.bed 9477907 200
_tmp.00020.bed 10026804 200
_tmp.00021.bed 9852814 200
_tmp.00022.bed 10545264 200
_tmp.00023.bed 9873209 200
_tmp.00024.bed 10288087 200
_tmp.00025.bed 10260838 200
_tmp.00026.bed 9614691 200
_tmp.00027.bed 10147634 200
_tmp.00028.bed 10106631 200
_tmp.00029.bed 10081432 200
_tmp.00030.bed 9766114 200
_tmp.00031.bed 10208732 200
_tmp.00032.bed 10246139 200
_tmp.00033.bed 10038728 200
_tmp.00034.bed 9581968 200
_tmp.00035.bed 9828160 200
_tmp.00036.bed 10130412 200
_tmp.00037.bed 10324249 200
_tmp.00038.bed 10381756 200
_tmp.00039.bed 10525373 200
_tmp.00040.bed 10265223 200
_tmp.00041.bed 9888666 200
_tmp.00042.bed 9932109 200
_tmp.00043.bed 9905693 200
_tmp.00044.bed 10677499 200
_tmp.00045.bed 9905825 200
_tmp.00046.bed 10611583 200
_tmp.00047.bed 10711877 200
_tmp.00048.bed 10311105 200
_tmp.00049.bed 9705714 200
_tmp.00050.bed 9636696 200
slpit.simple...\c
_tmp.00001.bed 468415 10
_tmp.00002.bed 470667 10
_tmp.00003.bed 576803 10
_tmp.00004.bed 442343 10
_tmp.00005.bed 434128 10
_tmp.00006.bed 374417 10
_tmp.00007.bed 502314 10
_tmp.00008.bed 588162 10
_tmp.00009.bed 540939 10
_tmp.00010.bed 422055 10
_tmp.00011.bed 625237 10
_tmp.00012.bed 417056 10
_tmp.00013.bed 527502 10
_tmp.00014.bed 504938 10
_tmp.00015.bed 532604 10
_tmp.00016.bed 521368 10
_tmp.00017.bed 622310 10
_tmp.00018.bed 545074 10
_tmp.00019.bed 459410 10
_tmp.00020.bed 398474 10
_tmp.00021.bed 403440 10
_tmp.00022.bed 616346 10
_tmp.00023.bed 564497 10
_tmp.00024.bed 650955 10
_tmp.00025.bed 427841 10
_tmp.00026.bed 506748 10
_tmp.00027.bed 387509 10
_tmp.00028.bed 594428 10
_tmp.00029.bed 551130 10
_tmp.00030.bed 616743 10
_tmp.00031.bed 531332 10
_tmp.00032.bed 574135 10
_tmp.00033.bed 524511 10
_tmp.00034.bed 364971 10
_tmp.00035.bed 472693 10
_tmp.00036.bed 518645 10
_tmp.00037.bed 541743 10
_tmp.00038.bed 495819 10
_tmp.00039.bed 414162 10
_tmp.00040.bed 460261 10
_tmp.00041.bed 397221 10
_tmp.00042.bed 505880 10
_tmp.00043.bed 463287 10
_tmp.00044.bed 608209 10
_tmp.00045.bed 561398 10
_tmp.00046.bed 553397 10
_tmp.00047.bed 523307 10
_tmp.00048.bed 561019 10
_tmp.00049.bed 538071 10
_tmp.00050.bed 561791 10
_tmp.00051.bed 489064 10
_tmp.00052.bed 439076 10
_tmp.00053.bed 654403 10
_tmp.00054.bed 625164 10
_tmp.00055.bed 493382 10
_tmp.00056.bed 463860 10
_tmp.00057.bed 407378 10
_tmp.00058.bed 328833 10
_tmp.00059.bed 535666 10
_tmp.00060.bed 450513 10
_tmp.00061.bed 576405 10
_tmp.00062.bed 522479 10
_tmp.00063.bed 537608 10
_tmp.00064.bed 494268 10
_tmp.00065.bed 536184 10
_tmp.00066.bed 479643 10
_tmp.00067.bed 506878 10
_tmp.00068.bed 439610 10
_tmp.00069.bed 445296 10
_tmp.00070.bed 402081 10
_tmp.00071.bed 601693 10
_tmp.00072.bed 433224 10
_tmp.00073.bed 593007 10
_tmp.00074.bed 329534 10
_tmp.00075.bed 723740 10
_tmp.00076.bed 303427 10
_tmp.00077.bed 360601 10
_tmp.00078.bed 630211 10
_tmp.00079.bed 632429 10
_tmp.00080.bed 518911 10
_tmp.00081.bed 628010 10
_tmp.00082.bed 545078 10
_tmp.00083.bed 354596 10
_tmp.00084.bed 546916 10
_tmp.00085.bed 461621 10
_tmp.00086.bed 499071 10
_tmp.00087.bed 518703 10
_tmp.00088.bed 578016 10
_tmp.00089.bed 618434 10
_tmp.00090.bed 463131 10
_tmp.00091.bed 629541 10
_tmp.00092.bed 316426 10
_tmp.00093.bed 476022 10
_tmp.00094.bed 637680 10
_tmp.00095.bed 372093 10
_tmp.00096.bed 594714 10
_tmp.00097.bed 537262 10
_tmp.00098.bed 480953 10
_tmp.00099.bed 543967 10
_tmp.00100.bed 593363 10
_tmp.00101.bed 476718 10
_tmp.00102.bed 567314 10
_tmp.00103.bed 648705 10
_tmp.00104.bed 554481 10
_tmp.00105.bed 501285 10
_tmp.00106.bed 361850 10
_tmp.00107.bed 504837 10
_tmp.00108.bed 690330 10
_tmp.00109.bed 345305 10
_tmp.00110.bed 479881 10
_tmp.00111.bed 465756 10
_tmp.00112.bed 395963 10
_tmp.00113.bed 476768 10
_tmp.00114.bed 647318 10
_tmp.00115.bed 422363 10
_tmp.00116.bed 479276 10
_tmp.00117.bed 460291 10
_tmp.00118.bed 441522 10
_tmp.00119.bed 288090 10
_tmp.00120.bed 551508 10
_tmp.00121.bed 607862 10
_tmp.00122.bed 491342 10
_tmp.00123.bed 498099 10
_tmp.00124.bed 605916 10
_tmp.00125.bed 411842 10
_tmp.00126.bed 518269 10
_tmp.00127.bed 428938 10
_tmp.00128.bed 495362 10
_tmp.00129.bed 443156 10
_tmp.00130.bed 547795 10
_tmp.00131.bed 507950 10
_tmp.00132.bed 411112 10
_tmp.00133.bed 554481 10
_tmp.00134.bed 445164 10
_tmp.00135.bed 333592 10
_tmp.00136.bed 467566 10
_tmp.00137.bed 625858 10
_tmp.00138.bed 421988 10
_tmp.00139.bed 496729 10
_tmp.00140.bed 486656 10
_tmp.00141.bed 533930 10
_tmp.00142.bed 585133 10
_tmp.00143.bed 437688 10
_tmp.00144.bed 615745 10
_tmp.00145.bed 338100 10
_tmp.00146.bed 607333 10
_tmp.00147.bed 662281 10
_tmp.00148.bed 566521 10
_tmp.00149.bed 487050 10
_tmp.00150.bed 435233 10
_tmp.00151.bed 579676 10
_tmp.00152.bed 643978 10
_tmp.00153.bed 491543 10
_tmp.00154.bed 446801 10
_tmp.00155.bed 311401 10
_tmp.00156.bed 441993 10
_tmp.00157.bed 455051 10
_tmp.00158.bed 567936 10
_tmp.00159.bed 636069 10
_tmp.00160.bed 469183 10
_tmp.00161.bed 401514 10
_tmp.00162.bed 552874 10
_tmp.00163.bed 431358 10
_tmp.00164.bed 333255 10
_tmp.00165.bed 442236 10
_tmp.00166.bed 317695 10
_tmp.00167.bed 486911 10
_tmp.00168.bed 440336 10
_tmp.00169.bed 420929 10
_tmp.00170.bed 435905 10
_tmp.00171.bed 536818 10
_tmp.00172.bed 537410 10
_tmp.00173.bed 391515 10
_tmp.00174.bed 551843 10
_tmp.00175.bed 591703 10
_tmp.00176.bed 387440 10
_tmp.00177.bed 724595 10
_tmp.00178.bed 431826 10
_tmp.00179.bed 586966 10
_tmp.00180.bed 330876 10
_tmp.00181.bed 441995 10
_tmp.00182.bed 527838 10
_tmp.00183.bed 465629 10
_tmp.00184.bed 418063 10
_tmp.00185.bed 518715 10
_tmp.00186.bed 599207 10
_tmp.00187.bed 601755 10
_tmp.00188.bed 650806 10
_tmp.00189.bed 507757 10
_tmp.00190.bed 660962 10
_tmp.00191.bed 357577 10
_tmp.00192.bed 406050 10
_tmp.00193.bed 403106 10
_tmp.00194.bed 583986 10
_tmp.00195.bed 551537 10
_tmp.00196.bed 662316 10
_tmp.00197.bed 386834 10
_tmp.00198.bed 478725 10
_tmp.00199.bed 677835 10
_tmp.00200.bed 409440 10
_tmp.00201.bed 393358 10
_tmp.00202.bed 637109 10
_tmp.00203.bed 434504 10
_tmp.00204.bed 533563 10
_tmp.00205.bed 494476 10
_tmp.00206.bed 757164 10
_tmp.00207.bed 542802 10
_tmp.00208.bed 500593 10
_tmp.00209.bed 483277 10
_tmp.00210.bed 531899 10
_tmp.00211.bed 480468 10
_tmp.00212.bed 568662 10
_tmp.00213.bed 448905 10
_tmp.00214.bed 359141 10
_tmp.00215.bed 418308 10
_tmp.00216.bed 503597 10
_tmp.00217.bed 477694 10
_tmp.00218.bed 393992 10
_tmp.00219.bed 596807 10
_tmp.00220.bed 492508 10
_tmp.00221.bed 391250 10
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Testing bedtools spacing:
spacing.t01...\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
make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/«PKGBUILDDIR»'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.24.0
CURRENT_VERSION = v2.24.0
* 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'.
- Building in src/utils/FileRecordTools/FileReaders
make[2]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools/Records
make[2]: Nothing to be done for 'all'.
- 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]: Nothing to be done for 'all'.
- 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/utils/ToolBase
make[2]: '../../../obj//ToolBase.o' is up to date.
- Building in src/utils/aux
make[2]: Nothing to be done for 'all'.
- 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/closestFile
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/coverageFile
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/fisher
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/spacingFile
make[2]: Nothing to be done for 'all'.
- Building in src/split
make[2]: Nothing to be done for 'all'.
- Building in src/subtractFile
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.
mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/local/bin
for file in bin/* ; do \
cp -f $file /«PKGBUILDDIR»/debian/tmp/usr/local/bin; \
done
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_install
install -d debian/bedtools/usr/bin
cp --reflink=auto -a ./bin/annotateBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bamToBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bamToFastq debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bedpeToBam debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bedToBam debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bedToIgv debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/bedtools debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/closestBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/clusterBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/complementBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/coverageBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/expandCols debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/fastaFromBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/flankBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/getOverlap debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/groupBy debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/intersectBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/linksBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/mapBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/mergeBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/multiBamCov debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/nucBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/pairToBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/pairToPair debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/randomBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/shuffleBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/slopBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/sortBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/subtractBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/tagBam debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/windowBed debian/bedtools/usr/bin/
cp --reflink=auto -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/
install -d debian/bedtools//usr/share/bash-completion/completions
cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools//usr/share/bash-completion/completions/
rm -f /«PKGBUILDDIR»/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
# make sure all *.sh files are featuring a '#!/bin/bash' as first line
# since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh}
# requiring bash this is taken for all scripts instead of checking first via /bin/sh -n
for sh in `find /«PKGBUILDDIR»/debian -name "*.sh"` ; do \
if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \
sed -i '1 i #!/bin/bash' ${sh} ; \
fi ; \
done
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installdocs -a
install -d debian/bedtools/usr/share/doc/bedtools
cp --reflink=auto -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 -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_installchangelogs RELEASE_HISTORY
install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
install -p -m0644 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 0644
find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
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 0644
find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/bedtools/usr/lib/arm-linux-gnueabihf/perl5/5.20 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
find /«PKGBUILDDIR»/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find /«PKGBUILDDIR»/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
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 -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
dh_gencontrol -a
echo misc:Depends= >> debian/bedtools.substvars
echo misc:Pre-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 0644 debian/bedtools/DEBIAN/control
chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -a
(cd debian/bedtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 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_2.24.0-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedtools_2.24.0-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build bedtools-2.24.0
dpkg-source: info: using options from bedtools-2.24.0/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150722-0559
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.24.0-2_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Thu, 16 Jul 2015 14:33:38 +0200
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.24.0-2
Distribution: stretch-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
Closes: 791830
Changes:
bedtools (2.24.0-2) unstable; urgency=medium
.
* Tests need bgzip from tabix package
* Add missing input files for tests
* link to genomes files in autopkgtests to enable more tests passing
* Fix MIPS build issue (Thanks for picking the patch from upstream
Arturo Borrero Gonzalez <arturo.borrero.glez@gmail.com>)
Closes: #791830
Checksums-Sha1:
0f25e85b46574dd990715d58be987f52b0ddfba7 507594 bedtools_2.24.0-2_armhf.deb
Checksums-Sha256:
7f3c6fbf07c72a19c57f5462ceb9c52a0c66c2c0893eb70dea04a5b91859742e 507594 bedtools_2.24.0-2_armhf.deb
Files:
ceb1c0d333eeb4a30d83a611f22d644d 507594 science optional bedtools_2.24.0-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.24.0-2_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 507594 bytes: control archive=2145 bytes.
836 bytes, 18 lines control
2748 bytes, 47 lines md5sums
Package: bedtools
Version: 2.24.0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1762
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 2015-07-22 05:58 ./
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/bin/
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2015-07-22 05:58 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2015-07-22 05:58 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2015-07-22 05:58 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2015-07-22 05:58 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1756400 2015-07-22 05:58 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2015-07-22 05:58 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2015-07-22 05:58 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2015-07-22 05:58 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2015-07-22 05:58 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2015-07-22 05:58 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2015-07-22 05:58 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2015-07-22 05:58 ./usr/bin/getOverlap
-rwxr-xr-x root/root 42 2015-07-22 05:58 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2015-07-22 05:58 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2015-07-22 05:58 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2015-07-22 05:58 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2015-07-22 05:58 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2015-07-22 05:58 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2015-07-22 05:58 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2015-07-22 05:58 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2015-07-22 05:58 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2015-07-22 05:58 ./usr/bin/randomBed
-rwxr-xr-x root/root 40 2015-07-22 05:58 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2015-07-22 05:58 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2015-07-22 05:58 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2015-07-22 05:58 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2015-07-22 05:58 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2015-07-22 05:58 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2015-07-22 05:58 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2015-07-22 05:58 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2015-07-16 12:33 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2015-05-28 00:44 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 856 2015-05-28 00:44 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1972 2015-05-28 00:44 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11672 2015-05-28 00:44 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1607 2015-05-28 00:44 ./usr/share/bedtools/genomes/mouse.mm10.genome.txt
-rw-r--r-- root/root 565 2015-05-28 00:44 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 585 2015-05-28 00:44 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-22 05:58 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3346 2015-05-28 00:44 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 2274 2015-07-16 12:33 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 15699 2015-05-28 00:44 ./usr/share/doc/bedtools/changelog.gz
-rw-r--r-- root/root 5353 2015-07-16 12:33 ./usr/share/doc/bedtools/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 65160
Build-Time: 1391
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 233
Job: bedtools_2.24.0-2
Machine Architecture: armhf
Package: bedtools
Package-Time: 1693
Source-Version: 2.24.0-2
Space: 65160
Status: successful
Version: 2.24.0-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150722-0559
Build needed 00:28:13, 65160k disc space