bedtools →
2.26.0+dfsg-3 →
armhf → 2016-11-26 05:05:07
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| bedtools 2.26.0+dfsg-3 (armhf) Sat, 26 Nov 2016 04:25:46 +0000 |
+==============================================================================+
Package: bedtools
Version: 2.26.0+dfsg-3
Source Version: 2.26.0+dfsg-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-58aa78df-5037-4561-85e2-485fd60240ad' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9530 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/bedtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/bedtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 13.5 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main bedtools 2.26.0+dfsg-3 (dsc) [2115 B]
Get:2 http://172.17.0.1/private stretch-staging/main bedtools 2.26.0+dfsg-3 (tar) [13.4 MB]
Get:3 http://172.17.0.1/private stretch-staging/main bedtools 2.26.0+dfsg-3 (diff) [51.6 kB]
Fetched 13.5 MB in 2s (5198 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedtools-waTwwd/bedtools-2.26.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedtools-waTwwd' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-yY4Qwz/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yY4Qwz/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Packages [433 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 libsasl2-modules libssl1.0.2 manpages
netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 13399 files and directories currently installed.)
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), python, zlib1g-dev, samtools
Filtered Build-Depends: debhelper (>= 9), python, zlib1g-dev, samtools
dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-bedtools-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Sources [506 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ Packages [587 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bedtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 libsasl2-modules manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts1 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts1 libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
samtools sbuild-build-depends-bedtools-dummy zlib1g-dev
0 upgraded, 53 newly installed, 0 to remove and 4 not upgraded.
Need to get 24.8 MB/24.9 MB of archives.
After this operation, 86.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yY4Qwz/apt_archive ./ sbuild-build-depends-bedtools-dummy 0.invalid.0 [796 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-3 [388 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-3 [1174 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-3 [1843 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-3 [279 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-1 [2527 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.16.0-1 [72.5 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-3+rpi1 [216 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-3 [220 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Unpacking sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.16.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.2-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up po-debconf (1.0.20) ...
Setting up python2.7 (2.7.12-3) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up python (2.7.11-2) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up libhts1:armhf (1.3.1-3+rpi1) ...
Setting up samtools (1.3.1-3) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161108-1 dpkg-dev_1.18.15 g++-6_6.2.0-13+rpi1 gcc-6_6.2.0-13+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-13+rpi1 libstdc++6_6.2.0-13+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.6+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161108-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-13+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-9 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-13+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.0-13+rpi1 gcc-6-base_6.2.0-13+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-9 gnupg-agent_2.1.15-9 gnupg-l10n_2.1.15-9 gpgv_2.1.15-9 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libadns1_1.5.0~rc1-1 libapparmor1_2.10.95-6 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-13+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-13+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.73-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-13+rpi1 libgcc1_1:6.2.0-13+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.2-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.6-4 libgomp1_6.2.0-13+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.3-1 libhts1_1.3.1-3+rpi1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.16.0-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-9 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules-db_2.1.27~72-g88d82a3+dfsg-1 libseccomp2_2.3.1-2 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.1-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1+rpi1 libstdc++-6-dev_6.2.0-13+rpi1 libstdc++6_6.2.0-13+rpi1 libsystemd0_232-3 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.0-13+rpi1 libudev1_232-3 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20161101+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-3 python2.7-minimal_2.7.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 samtools_1.3.1-3 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-3 systemd-sysv_232-3 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016i-1 udev_232-3 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 7 13:05:05 2016 UTC
gpgv: using RSA key C5BD6C8F2295D502
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedtools_2.26.0+dfsg-3.dsc
dpkg-source: info: extracting bedtools in /<<BUILDDIR>>/bedtools-2.26.0+dfsg
dpkg-source: info: unpacking bedtools_2.26.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking bedtools_2.26.0+dfsg-3.debian.tar.xz
dpkg-source: info: applying gzstream.h.patch
dpkg-source: info: applying fix_test_script.patch
dpkg-source: info: applying remove_barski_binding_site.png.patch
dpkg-source: info: applying reproducible_build.patch
dpkg-source: info: applying v2.26.0-19-g6bf23c4.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
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-58aa78df-5037-4561-85e2-485fd60240ad
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bedtools
dpkg-buildpackage: info: source version 2.26.0+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build bedtools-2.26.0+dfsg
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from bedtools-2.26.0+dfsg/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
* Cleaning-up BamTools API
* Cleaning up.
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_clean
rm -f debian/debhelper-build-stamp
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_update_autotools_config -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.26.0
CURRENT_VERSION =
Updating version file.
* Creating BamTools API
- 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/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
ContextBase.cpp: In constructor 'ContextBase::ContextBase()':
ContextBase.cpp:71:38: warning: passing NULL to non-pointer argument 1 of 'std::vector<_Tp, _Alloc>::vector(std::vector<_Tp, _Alloc>::size_type, const allocator_type&) [with _Tp = FileRecordMgr*; _Alloc = std::allocator<FileRecordMgr*>; std::vector<_Tp, _Alloc>::size_type = unsigned int; std::vector<_Tp, _Alloc>::allocator_type = std::allocator<FileRecordMgr*>]' [-Wconversion-null]
_nameConventionWarningTripped(false)
^
* 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/general
* compiling ParseTools.cpp
* 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/gzstream/ -Isrc/utils/lineFileUtilities -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
* compiling FileRecordTypeChecker.cpp
FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
FileRecordTypeChecker.cpp:355:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j < len; j++) {
~~^~~~~
- 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
src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const':
src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
return m_ip4Address < m_ip4Address;
~~~~~~~~~~~~~^~~~~~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const':
src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if ( i != 0 )
^~
src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
^~
* 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
genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)':
genomeCoverageBed.cpp:322:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
~~~^~~~~~~~~~~~~~
- 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
intersectFile.cpp: In member function 'virtual void IntersectFile::processHits(RecordOutputMgr*, RecordKeyVector&)':
intersectFile.cpp:70:33: warning: variable 'hitListIter' set but not used [-Wunused-but-set-variable]
RecordKeyVector::iterator_type hitListIter = hits.begin();
^~~~~~~~~~~
- 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/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/shiftBed
* compiling shiftBedMain.cpp
* compiling shiftBed.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:85:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:107:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ( ((int)bed.end + (long)_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 '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_auto_test -a
make -j1 test
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.26.0
CURRENT_VERSION = v2.26.0
* Creating BamTools API
- 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/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/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/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/shiftBed
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.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
general.t43...\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
closest.t60...\c
ok
closest.t61...\c
ok
closest.t62...\c
ok
closest.t63...\c
ok
closest.t64...\c
ok
closest.t65...\c
ok
closest.t66...\c
ok
closest.t67...\c
ok
closest.t68...\c
ok
closest.t69...\c
ok
closest.t70...\c
ok
closest.t71...\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
ok
coverage.t2...\c
ok
ok
coverage.t3...\c
ok
ok
coverage.t4...\c
ok
ok
coverage.t5...\c
ok
ok
coverage.t6...\c
ok
ok
coverage.t7...\c
ok
ok
coverage.t8...\c
ok
ok
coverage.t9...\c
ok
ok
coverage.t10...\c
ok
ok
coverage.t11...\c
ok
ok
coverage.t12...\c
ok
ok
coverage.t13...\c
ok
ok
coverage.t14...\c
ok
ok
coverage.t15...\c
ok
ok
coverage.t16...\c
ok
ok
coverage.t17...\c
ok
ok
coverage.t18...\c
ok
ok
coverage.t19...\c
ok
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
14c14
< 1 1 1 nan
---
> 1 1 1 -nan
fail
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
ok
genomecov.t12...\c
ok
genomecov.t13...\c
ok
genomecov.t14...\c
ok
genomecov.t15...\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
getfasta.t11...\c
ok
getfasta.t12...\c
ok
getfasta.t13...\c
ok
getfasta.t134..\c
ok
Testing bedtools groupby:
test.sh: line 35: cd: groupby: No such file or directory
bash: test-groupby.sh: No such file or directory
Testing bedtools intersect:
test.sh: line 38: cd: intersect: No such file or directory
bash: test-intersect.sh: No such file or directory
bash: new_test-intersect.sh: No such file or directory
Testing bedtools jaccard:
test.sh: line 41: cd: jaccard: No such file or directory
bash: test-jaccard.sh: No such file or directory
Testing bedtools map:
test.sh: line 44: cd: map: No such file or directory
bash: test-map.sh: No such file or directory
Testing bedtools merge:
test.sh: line 47: cd: merge: No such file or directory
bash: test-merge.sh: No such file or directory
Testing bedtools multicov:
test.sh: line 50: cd: multicov: No such file or directory
bash: test-multicov.sh: No such file or directory
Testing bedtools reldist:
test.sh: line 53: cd: reldist: No such file or directory
bash: test-reldist.sh: No such file or directory
Testing bedtools shift:
test.sh: line 56: cd: shift: No such file or directory
bash: test-shift.sh: No such file or directory
Testing bedtools slop:
test.sh: line 59: cd: slop: No such file or directory
bash: test-slop.sh: No such file or directory
Testing bedtools sort:
test.sh: line 62: cd: slop: No such file or directory
bash: test-sort.sh: No such file or directory
Testing bedtools shuffle:
test.sh: line 65: cd: shuffle: No such file or directory
bash: test-shuffle.sh: No such file or directory
Testing bedtools subtract:
test.sh: line 68: cd: subtract: No such file or directory
bash: test-subtract.sh: No such file or directory
Testing bedtools sample:
test.sh: line 71: cd: sample: No such file or directory
bash: test-sample.sh: No such file or directory
Testing bedtools split:
test.sh: line 74: cd: split: No such file or directory
bash: test-split.sh: No such file or directory
Testing bedtools spacing:
test.sh: line 77: cd: spacing: No such file or directory
bash: test-spacing.sh: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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=/<<BUILDDIR>>/bedtools-2.26.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.26.0
CURRENT_VERSION = v2.26.0
* Creating BamTools API
- 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/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/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/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/shiftBed
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 /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian/tmp/usr/local/bin
for file in bin/* ; do \
cp -f $file /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian/tmp/usr/local/bin; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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/shiftBed 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 /<<BUILDDIR>>/bedtools-2.26.0+dfsg/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 /<<BUILDDIR>>/bedtools-2.26.0+dfsg/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 '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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 '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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 '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/bedtools
chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
cd '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
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 -type f -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/usr/lib/arm-linux-gnueabihf/perl5/5.24 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/bedtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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 /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome
find /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find /<<BUILDDIR>>/bedtools-2.26.0+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/bedtools-2.26.0+dfsg'
dh_strip -a
install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/76
objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/76/ebe611bfa97a57101ed93f033f24be30504df6.debug
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/76/ebe611bfa97a57101ed93f033f24be30504df6.debug
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/76/ebe611bfa97a57101ed93f033f24be30504df6.debug
strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/76/ebe611bfa97a57101ed93f033f24be30504df6.debug debian/bedtools/usr/bin/bedtools
install -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc
ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym
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
install -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN
dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=Debug symbols for bedtools" -DBuild-Ids=76ebe611bfa97a57101ed93f033f24be30504df6 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control
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
(cd debian/.debhelper/bedtools/dbgsym-root >/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/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/bedtools/dbgsym-root ..
dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.26.0+dfsg-3_armhf.deb'.
dpkg-deb --build debian/bedtools ..
dpkg-deb: building package 'bedtools' in '../bedtools_2.26.0+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bedtools_2.26.0+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build bedtools-2.26.0+dfsg
dpkg-source: info: using options from bedtools-2.26.0+dfsg/debian/source/options: --single-debian-patch
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-11-26T05:01:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedtools_2.26.0+dfsg-3_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sat, 05 Nov 2016 21:48:09 +0900
Source: bedtools
Binary: bedtools bedtools-test
Architecture: armhf
Version: 2.26.0+dfsg-3
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
Closes: 831833
Changes:
bedtools (2.26.0+dfsg-3) unstable; urgency=medium
.
d6d3452 Sync with upstream repo at commit 6bf23c, closes: #831833.
Checksums-Sha1:
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a9c4bc35edcafb035b7d3c1e5263856173d49054 5427 bedtools_2.26.0+dfsg-3_armhf.buildinfo
be79ec958e99fdb13b01eb0cb2a9540f9df04f9f 482836 bedtools_2.26.0+dfsg-3_armhf.deb
Checksums-Sha256:
0d7199d85da11348253f27dde92ebd36d9cc023e27127b29f032da2e49a4ffea 63338 bedtools-dbgsym_2.26.0+dfsg-3_armhf.deb
1daa7601641fca98d2d2a940487b22990605eaf231bd48a882a484d8fc8a06e6 5427 bedtools_2.26.0+dfsg-3_armhf.buildinfo
2216f807c8d17d5fbc6a122366441d878977650cb8cf2c612fa022453c05b966 482836 bedtools_2.26.0+dfsg-3_armhf.deb
Files:
464a9203c944ba97f34322ef4a8a7ffc 63338 debug extra bedtools-dbgsym_2.26.0+dfsg-3_armhf.deb
e642ee869d955c8ae1cf9f1306a0cae8 5427 science optional bedtools_2.26.0+dfsg-3_armhf.buildinfo
fdc97473afaa02abcfc1a980f8c1f29f 482836 science optional bedtools_2.26.0+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedtools-dbgsym_2.26.0+dfsg-3_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 63338 bytes: control archive=489 bytes.
428 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: bedtools-dbgsym
Source: bedtools
Version: 2.26.0+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 365
Depends: bedtools (= 2.26.0+dfsg-3)
Section: debug
Priority: extra
Homepage: https://github.com/arq5x/bedtools2
Description: Debug symbols for bedtools
Auto-Built-Package: debug-symbols
Build-Ids: 76ebe611bfa97a57101ed93f033f24be30504df6
drwxr-xr-x root/root 0 2016-11-05 12:48 ./
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/lib/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/lib/debug/.build-id/76/
-rw-r--r-- root/root 362576 2016-11-05 12:48 ./usr/lib/debug/.build-id/76/ebe611bfa97a57101ed93f033f24be30504df6.debug
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-11-05 12:48 ./usr/share/doc/bedtools-dbgsym -> bedtools
bedtools_2.26.0+dfsg-3_armhf.deb
--------------------------------
new debian package, version 2.0.
size 482836 bytes: control archive=2079 bytes.
840 bytes, 18 lines control
2795 bytes, 48 lines md5sums
Package: bedtools
Version: 2.26.0+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1630
Depends: libc6 (>= 2.23), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Suggests: filo
Section: science
Priority: optional
Homepage: https://github.com/arq5x/bedtools2
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 2016-11-05 12:48 ./
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/bin/
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/annotateBed
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/bamToBed
-rwxr-xr-x root/root 43 2016-11-05 12:48 ./usr/bin/bamToFastq
-rwxr-xr-x root/root 44 2016-11-05 12:48 ./usr/bin/bed12ToBed6
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/bedToBam
-rwxr-xr-x root/root 36 2016-11-05 12:48 ./usr/bin/bedToIgv
-rwxr-xr-x root/root 43 2016-11-05 12:48 ./usr/bin/bedpeToBam
-rwxr-xr-x root/root 1570488 2016-11-05 12:48 ./usr/bin/bedtools
-rwxr-xr-x root/root 40 2016-11-05 12:48 ./usr/bin/closestBed
-rwxr-xr-x root/root 40 2016-11-05 12:48 ./usr/bin/clusterBed
-rwxr-xr-x root/root 43 2016-11-05 12:48 ./usr/bin/complementBed
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/coverageBed
-rwxr-xr-x root/root 39 2016-11-05 12:48 ./usr/bin/expandCols
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/fastaFromBed
-rwxr-xr-x root/root 38 2016-11-05 12:48 ./usr/bin/flankBed
-rwxr-xr-x root/root 42 2016-11-05 12:48 ./usr/bin/genomeCoverageBed
-rwxr-xr-x root/root 40 2016-11-05 12:48 ./usr/bin/getOverlap
-rwxr-xr-x root/root 42 2016-11-05 12:48 ./usr/bin/intersectBed
-rwxr-xr-x root/root 38 2016-11-05 12:48 ./usr/bin/linksBed
-rwxr-xr-x root/root 36 2016-11-05 12:48 ./usr/bin/mapBed
-rwxr-xr-x root/root 42 2016-11-05 12:48 ./usr/bin/maskFastaFromBed
-rwxr-xr-x root/root 38 2016-11-05 12:48 ./usr/bin/mergeBed
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/multiBamCov
-rwxr-xr-x root/root 43 2016-11-05 12:48 ./usr/bin/multiIntersectBed
-rwxr-xr-x root/root 36 2016-11-05 12:48 ./usr/bin/nucBed
-rwxr-xr-x root/root 42 2016-11-05 12:48 ./usr/bin/pairToBed
-rwxr-xr-x root/root 43 2016-11-05 12:48 ./usr/bin/pairToPair
-rwxr-xr-x root/root 39 2016-11-05 12:48 ./usr/bin/randomBed
-rwxr-xr-x root/root 38 2016-11-05 12:48 ./usr/bin/shiftBed
-rwxr-xr-x root/root 40 2016-11-05 12:48 ./usr/bin/shuffleBed
-rwxr-xr-x root/root 37 2016-11-05 12:48 ./usr/bin/slopBed
-rwxr-xr-x root/root 37 2016-11-05 12:48 ./usr/bin/sortBed
-rwxr-xr-x root/root 41 2016-11-05 12:48 ./usr/bin/subtractBed
-rwxr-xr-x root/root 36 2016-11-05 12:48 ./usr/bin/tagBam
-rwxr-xr-x root/root 42 2016-11-05 12:48 ./usr/bin/unionBedGraphs
-rwxr-xr-x root/root 39 2016-11-05 12:48 ./usr/bin/windowBed
-rwxr-xr-x root/root 44 2016-11-05 12:48 ./usr/bin/windowMaker
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 638 2016-07-20 00:12 ./usr/share/bash-completion/completions/bedtools
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/bedtools/
drwxr-xr-x root/root 0 2016-07-06 22:23 ./usr/share/bedtools/genomes/
-rw-r--r-- root/root 868 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg18.genome
-rw-r--r-- root/root 1984 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg19.genome
-rw-r--r-- root/root 11684 2016-07-06 22:23 ./usr/share/bedtools/genomes/human.hg38.genome
-rw-r--r-- root/root 1417 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm10.genome
-rw-r--r-- root/root 577 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm8.genome
-rw-r--r-- root/root 596 2016-07-06 22:23 ./usr/share/bedtools/genomes/mouse.mm9.genome
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-11-05 12:48 ./usr/share/doc/bedtools/
-rw-r--r-- root/root 3244 2016-07-06 22:23 ./usr/share/doc/bedtools/README.md
-rw-r--r-- root/root 2740 2016-11-05 12:48 ./usr/share/doc/bedtools/changelog.Debian.gz
-rw-r--r-- root/root 15699 2016-07-06 22:23 ./usr/share/doc/bedtools/changelog.gz
-rw-r--r-- root/root 5546 2016-11-05 11:40 ./usr/share/doc/bedtools/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 67500
Build-Time: 1802
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 278
Job: bedtools_2.26.0+dfsg-3
Machine Architecture: armhf
Package: bedtools
Package-Time: 2140
Source-Version: 2.26.0+dfsg-3
Space: 67500
Status: successful
Version: 2.26.0+dfsg-3
--------------------------------------------------------------------------------
Finished at 2016-11-26T05:01:26Z
Build needed 00:35:40, 67500k disc space