bedtools →
2.25.0-1 →
armhf → 2015-09-12 22:20:01
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ bedtools 2.25.0-1 (armhf) 12 Sep 2015 21:52 ║
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Package: bedtools
Version: 2.25.0-1
Source Version: 2.25.0-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/bedtools-NMl8vM/bedtools-2.25.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/bedtools-NMl8vM' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-d4a3560d-ce8b-4636-8c22-2846d800a743' with '«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 [8323 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
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NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/bedtools.git
Need to get 19.6 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main bedtools 2.25.0-1 (dsc) [2071 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main bedtools 2.25.0-1 (tar) [19.6 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bedtools 2.25.0-1 (diff) [8132 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-LjaqGH/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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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
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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-hKWwIM/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
libasprintf0v5 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
libasprintf0v5 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 0 not upgraded.
Need to get 14.5 MB/14.5 MB of archives.
After this operation, 45.9 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.2-1 [973 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0v5 armhf 0.19.5.1-1 [32.0 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 3.59 [36.4 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.11.1-1 [391 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 0.19.5.1-1 [118 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.5.1-1 [1386 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 9.20150811 [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+b1 [197 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
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Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc-4.9_4.9.3-4 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-4 cpp-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-4 g++-5_5.2.1-16+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9_4.9.3-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-16+rpi1 gcc-5-base_5.2.1-16+rpi1 gettext_0.19.5.1-1 gettext-base_0.19.5.1-1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libasan1_4.9.3-4 libasan2_5.2.1-16+rpi1 libasprintf0v5_0.19.5.1-1 libatomic1_5.2.1-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-16+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.8.20-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.3-4 libgcc-5-dev_5.2.1-16+rpi1 libgcc1_1:5.2.1-16+rpi1 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-7+rpi1 libgomp1_5.2.1-16+rpi1 libgpg-error0_1.19-2 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.05-9 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncursesw5_6.0+20150810-1 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_2:8.35-7.1 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-3 libpython2.7-stdlib_2.7.10-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2+b1 libsmartcols1_2.26.2-9 libsqlite3-0_3.8.11.1-1 libss2_1.42.13-1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 libsystemd0_225-1 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20150810-1 libubsan0_5.2.1-16+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.2-1 mawk_1.3.3-17 mime-support_3.59 mount_2.26.2-9 mountall_2.54 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.10-2 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_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-1 tzdata_2015f-1 udev_225-1 util-linux_2.26.2-9 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Sep 4 15:45:52 2015 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bedtools_2.25.0-1.dsc
dpkg-source: info: extracting bedtools in bedtools-2.25.0
dpkg-source: info: unpacking bedtools_2.25.0.orig.tar.gz
dpkg-source: info: unpacking bedtools_2.25.0-1.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying fix_test_script.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-d4a3560d-ce8b-4636-8c22-2846d800a743
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
dpkg-buildpackage: source version 2.25.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build bedtools-2.25.0
dpkg-buildpackage: host architecture armhf
dpkg-source: info: using options from bedtools-2.25.0/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 = v2.25.0
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
* compiling ContextComplement.cpp
* compiling ContextGroupBy.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 PlusFields.cpp
* compiling BedPlusInterval.cpp
* compiling Bed12Interval.cpp
* compiling BamRecord.cpp
* compiling GffRecord.cpp
* compiling GffPlusRecord.cpp
* compiling VcfRecord.cpp
* compiling NoPosPlusRecord.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/driver -D_FORTIFY_SOURCE=2 -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
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
Fasta.cpp:290:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), seqlen, file);
^
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)':
Fasta.cpp:332:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(seq, sizeof(char), (off_t) seqlen, file);
^
* 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/driver
* 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/complementFile
* compiling complementHelp.cpp
* compiling complementFile.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
* compiling groupByHelp.cpp
- 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
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
^
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
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 = v2.25.0
CURRENT_VERSION = v2.25.0
* 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/driver
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/complementFile
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
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
^
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
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
coverage.t11...\c
ok
coverage.t12...\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
genomecov.t8...\c
ok
genomecov.t9...\c
ok
genomecov.t10...\c
ok
genomecov.t11...\c
Error: The requested genome file (genome.txt) could not be opened. Exiting!
0a1,8
> 1 0 93 100 0.93
> 1 1 4 100 0.04
> 1 2 3 100 0.03
> 2 0 100 100 1
> 3 0 100 100 1
> genome 0 293 300 0.976667
> genome 1 4 300 0.0133333
> genome 2 3 300 0.01
fail
genomecov.t12...\c
Error: The requested genome file (genome.txt) could not be opened. Exiting!
0a1,3
> 1 15 17 1
> 1 17 20 2
> 1 20 22 1
fail
genomecov.t13...\c
Error: The requested genome file (genome.txt) could not be opened. Exiting!
0a1,7
> 1 0 15 0
> 1 15 17 1
> 1 17 20 2
> 1 20 22 1
> 1 22 100 0
> 2 0 100 0
> 3 0 100 0
fail
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
ok
intersect.t49...\c
ok
intersect.t50...\c
ok
intersect.t51...\c
ok
intersect.t52...\c
ok
intersect.t53...\c
1d0
< \c
fail
intersect.t54...\c
ok
intersect.t55...\c
1d0
< \c
fail
intersect.t56...\c
ok
intersect.t57...\c
ok
intersect.t58...\c
ok
intersect.t59...\c
1d0
< \c
fail
intersect.t60...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
*****
*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option.
*****
1d0
< \c
fail
intersect.t61...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
*****
*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option.
*****
ok
intersect.t62...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
*****
*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option.
*****
ok
intersect.t63...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
*****
*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option.
*****
ok
intersect.t64...\c
[bam_header_read] EOF marker is absent. The input is probably truncated.
*****
*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option.
*****
1d0
< \c
fail
intersect.t65...\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
map.t54...\c
ok
map.t55...\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
merge.t48...\c
ok
merge.t49...\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 sort:
bash: test-sort.sh: No such file or directory
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:
split.01.size...\c
1,10c1,10
< _tmp.00001.bed 9943540 200
< _tmp.00002.bed 9943482 201
< _tmp.00003.bed 9943541 200
< _tmp.00004.bed 9943561 200
< _tmp.00005.bed 9943471 200
< _tmp.00006.bed 9943475 200
< _tmp.00007.bed 9943468 200
< _tmp.00008.bed 9943487 200
< _tmp.00009.bed 9943539 200
< _tmp.00010.bed 9943531 200
---
> _tmp.00001.bed 9949426 201
> _tmp.00002.bed 9949437 201
> _tmp.00003.bed 9949548 200
> _tmp.00004.bed 9949432 201
> _tmp.00005.bed 9949493 200
> _tmp.00006.bed 9949442 200
> _tmp.00007.bed 9949437 201
> _tmp.00008.bed 9949514 200
> _tmp.00009.bed 9949497 200
> _tmp.00010.bed 9949573 200
fail
split.02.simple...\c
1,10c1,10
< _tmp.00001.bed 9952674 200
< _tmp.00002.bed 9751661 200
< _tmp.00003.bed 9649058 200
< _tmp.00004.bed 9929508 200
< _tmp.00005.bed 9556713 200
< _tmp.00006.bed 10298876 200
< _tmp.00007.bed 10043102 200
< _tmp.00008.bed 9781861 200
< _tmp.00009.bed 9502188 200
< _tmp.00010.bed 9991229 200
---
> _tmp.00001.bed 10279720 200
> _tmp.00002.bed 10012453 200
> _tmp.00003.bed 10392293 200
> _tmp.00004.bed 9581888 200
> _tmp.00005.bed 9452593 200
> _tmp.00006.bed 10295934 200
> _tmp.00007.bed 9529037 200
> _tmp.00008.bed 10064453 200
> _tmp.00009.bed 9053882 200
> _tmp.00010.bed 10031497 200
fail
spliit.03.simple...\c
1,10c1,10
< _tmp.00001.bed 414150 10
< _tmp.00002.bed 586843 10
< _tmp.00003.bed 503604 10
< _tmp.00004.bed 410044 10
< _tmp.00005.bed 499400 10
< _tmp.00006.bed 537341 10
< _tmp.00007.bed 698581 10
< _tmp.00008.bed 555258 10
< _tmp.00009.bed 474511 10
< _tmp.00010.bed 633012 10
---
> _tmp.00001.bed 461353 10
> _tmp.00002.bed 292997 10
> _tmp.00003.bed 495508 10
> _tmp.00004.bed 415252 10
> _tmp.00005.bed 576470 10
> _tmp.00006.bed 476563 10
> _tmp.00007.bed 383267 10
> _tmp.00008.bed 673383 10
> _tmp.00009.bed 411963 10
> _tmp.00010.bed 478964 10
fail
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 = v2.25.0
CURRENT_VERSION = v2.25.0
* 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/driver
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/complementFile
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
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(diffCmd.c_str());
^
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(sLine, 4192, fp);
^
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_2.25.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedtools_2.25.0-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build bedtools-2.25.0
dpkg-source: info: using options from bedtools-2.25.0/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150912-2219
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.25.0-1_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Fri, 04 Sep 2015 16:55:21 +0200
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.25.0-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
Changes:
bedtools (2.25.0-1) unstable; urgency=medium
.
e37865 Merge tag 'v2.25.0' into debian/unstable
Checksums-Sha1:
9403a10cf1c5bf8c3b182c97197acba315235714 470714 bedtools_2.25.0-1_armhf.deb
Checksums-Sha256:
e4baabada9374f433b8b21d0455bd8ab0122659f1b055c4a3966de7316a65ad9 470714 bedtools_2.25.0-1_armhf.deb
Files:
21bf0cd0667bd929f429623096777fff 470714 science optional bedtools_2.25.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
bedtools_2.25.0-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 470714 bytes: control archive=2053 bytes.
837 bytes, 18 lines control
2748 bytes, 47 lines md5sums
Package: bedtools
Version: 2.25.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1591
Depends: libc6 (>= 2.15), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 5.2), 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 2015-09-12 22:19 ./
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/bin/
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2015-09-12 22:19 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2015-09-12 22:19 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2015-09-12 22:19 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2015-09-12 22:19 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1531100 2015-09-12 22:19 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2015-09-12 22:19 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2015-09-12 22:19 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2015-09-12 22:19 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2015-09-12 22:19 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2015-09-12 22:19 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2015-09-12 22:19 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2015-09-12 22:19 ./usr/bin/getOverlap
-rwxr-xr-x root/root 42 2015-09-12 22:19 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2015-09-12 22:19 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2015-09-12 22:19 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2015-09-12 22:19 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2015-09-12 22:19 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2015-09-12 22:19 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2015-09-12 22:19 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2015-09-12 22:19 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2015-09-12 22:19 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2015-09-12 22:19 ./usr/bin/randomBed
-rwxr-xr-x root/root 40 2015-09-12 22:19 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2015-09-12 22:19 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2015-09-12 22:19 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2015-09-12 22:19 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2015-09-12 22:19 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2015-09-12 22:19 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2015-09-12 22:19 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2015-09-12 22:19 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2015-09-04 14:58 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2015-09-03 04:36 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 856 2015-09-03 04:36 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1972 2015-09-03 04:36 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11672 2015-09-03 04:36 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1607 2015-09-03 04:36 ./usr/share/bedtools/genomes/mouse.mm10.genome.txt
-rw-r--r-- root/root 565 2015-09-03 04:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 585 2015-09-03 04:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-12 22:19 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3397 2015-09-03 04:36 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 2306 2015-09-04 15:10 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 15699 2015-09-03 04:36 ./usr/share/doc/bedtools/changelog.gz
-rw-r--r-- root/root 5352 2015-09-04 15:08 ./usr/share/doc/bedtools/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 65580
Build-Time: 1360
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 235
Job: bedtools_2.25.0-1
Machine Architecture: armhf
Package: bedtools
Package-Time: 1662
Source-Version: 2.25.0-1
Space: 65580
Status: successful
Version: 2.25.0-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150912-2219
Build needed 00:27:42, 65580k disc space