[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.15.0-1-1-g61a9585
Charles Plessy
plessy at debian.org
Fri Mar 16 11:47:27 UTC 2012
The following commit has been merged in the meta branch:
commit 61a9585d73775abd43948540b88fc12a4f7ba747
Author: Charles Plessy <plessy at debian.org>
Date: Fri Mar 16 20:45:40 2012 +0900
bedtools (2.16.1-1) unstable; urgency=low
diff --git a/amd64.changes b/amd64.changes
index adfb010..b1709eb 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,42 +14,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 75d72beb9913c910f6e3cb4a536abd7760d05a8d 1975 bedtools_2.15.0-1.dsc
- ca0aa595809f56c3fb5752de32d7ceb87ea844de 962861 bedtools_2.15.0.orig.tar.gz
- d865eee05d8abe20118552c8e48581b648f2dd8d 4499 bedtools_2.15.0-1.debian.tar.gz
- 65f70842da0b9fbe376819cc9110beb7139a3beb 394858 bedtools_2.15.0-1_amd64.deb
+ 6bca39a2b902fc0ace16ecd46d14d116ad013ed8 1975 bedtools_2.16.1-1.dsc
+ 79b634a26e2cf56669d05068954a328eb73e2942 977886 bedtools_2.16.1.orig.tar.gz
+ e4f81f729a5ebaafe2855fd22a2e5814db725e35 5035 bedtools_2.16.1-1.debian.tar.gz
+ 6d2ae6496223289d24e7c80dfdbd42d97a5071b1 433932 bedtools_2.16.1-1_amd64.deb
Checksums-Sha256:
- 52d40a49a335a86f5edab07218905e8a2ff92c69e2f9a4d809de72f2ce625cde 1975 bedtools_2.15.0-1.dsc
- 2e6f20435ad403fdf0c9d4d8f160b7eb2491d5213935178c25d6ab222a45c505 962861 bedtools_2.15.0.orig.tar.gz
- 3d54090b1d3222ed865cbe517c57bc99e29f79e0514fa2ceeac703d3164532e9 4499 bedtools_2.15.0-1.debian.tar.gz
- 8f19b6993b3e467e51b92f1496aac16f51cb206780a96d2adb7526bb8690aa20 394858 bedtools_2.15.0-1_amd64.deb
+ 3e00376740ad4501cf112630227e0d5af22a64b4030925708d10496e28ad8a58 1975 bedtools_2.16.1-1.dsc
+ 6f6667d59719388d01c2c2dd51050998f6bef3e074b43a53df09b99dbe6cac6b 977886 bedtools_2.16.1.orig.tar.gz
+ 36ae723e7e464c74433e6c94a1aa1c71eff55486301b6e5689bf0959d7cdf9b3 5035 bedtools_2.16.1-1.debian.tar.gz
+ 2cf489420b39b2d8fb6539a3b5b534cebd8383d2678094cb86fa891bdccf68d3 433932 bedtools_2.16.1-1_amd64.deb
Files:
- ccb9602166fd9688ff05a62e02681397 1975 science optional bedtools_2.15.0-1.dsc
- c0cbcb748f54ed99fce47c687bd0f260 962861 science optional bedtools_2.15.0.orig.tar.gz
- 26766fd8ab3c709115cef6f5d28fb80f 4499 science optional bedtools_2.15.0-1.debian.tar.gz
- ca6f61f75be65643858e1b76599d9212 394858 science optional bedtools_2.15.0-1_amd64.deb
+ d7ce9220f9f237aa4100eb586265d989 1975 science optional bedtools_2.16.1-1.dsc
+ f9356528d6c70b2f25a91f0464a539f9 977886 science optional bedtools_2.16.1.orig.tar.gz
+ 5af58a135fb459c1e8513f7e9dc80d29 5035 science optional bedtools_2.16.1-1.debian.tar.gz
+ ddd0ee0ea1d713c064957da3f96944c4 433932 science optional bedtools_2.16.1-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index e729832..6919e15 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,18 +1,18 @@
sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (amd64) 11 Jan 2012 15:12 ║
+║ bedtools 2.16.1-1 (amd64) 16 Mar 2012 20:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bedtools-Sh4qF0/bedtools-2.15.0' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-Sh4qF0' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-343774b6-6dca-4595-80cd-b14edd2af35d' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bedtools-6FawjF/bedtools-2.16.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-6FawjF' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-1381889c-d61a-4c99-85bb-1dc3ce616ec9' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -21,6 +21,7 @@ I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-34
Hit http://ftp.jp.debian.org sid InRelease
Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
Hit http://ftp.jp.debian.org sid/main TranslationIndex
+Hit http://ftp.jp.debian.org sid/main Translation-en
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -35,14 +36,14 @@ Reading state information...
Local sources
─────────────
-bedtools_2.15.0-1.dsc exists in .; copying to chroot
+bedtools_2.16.1-1.dsc exists in .; copying to chroot
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-t_E5Ih/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-XHHn1l/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -58,7 +59,7 @@ sbuild-build-depends-core-dummy is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-XH46pP/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-X7aQ3O/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
Reading package lists...
@@ -90,32 +91,48 @@ The following NEW packages will be installed:
libxml2 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal quilt sbuild-build-depends-bedtools-dummy zlib1g-dev
0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded.
-Need to get 5163 kB/17.3 MB of archives.
-After this operation, 48.3 MB of additional disk space will be used.
-Get:1 http://ftp.jp.debian.org/debian/ sid/main libsqlite3-0 amd64 3.7.9-3 [431 kB]
-Get:2 http://ftp.jp.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.2-9 [1674 kB]
-Get:3 http://ftp.jp.debian.org/debian/ sid/main python2.7 amd64 2.7.2-9 [2647 kB]
-Get:4 http://ftp.jp.debian.org/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB]
-Get:5 http://ftp.jp.debian.org/debian/ sid/main quilt all 0.50-2 [381 kB]
+Need to get 12.0 MB/17.6 MB of archives.
+After this operation, 48.8 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ sid/main libpipeline1 amd64 1.2.1-1 [39.2 kB]
+Get:2 http://ftp.jp.debian.org/debian/ sid/main libssl1.0.0 amd64 1.0.0h-1 [1146 kB]
+Get:3 http://ftp.jp.debian.org/debian/ sid/main libmagic1 amd64 5.10-1 [248 kB]
+Get:4 http://ftp.jp.debian.org/debian/ sid/main libglib2.0-0 amd64 2.30.2-6 [1846 kB]
+Get:5 http://ftp.jp.debian.org/debian/ sid/main libxml2 amd64 2.7.8.dfsg-7 [895 kB]
+Get:6 http://ftp.jp.debian.org/debian/ sid/main libcroco3 amd64 0.6.4-2 [150 kB]
+Get:7 http://ftp.jp.debian.org/debian/ sid/main man-db amd64 2.6.1-1 [1057 kB]
+Get:8 http://ftp.jp.debian.org/debian/ sid/main file amd64 5.10-1 [53.0 kB]
+Get:9 http://ftp.jp.debian.org/debian/ sid/main libsqlite3-0 amd64 3.7.10-1 [436 kB]
+Get:10 http://ftp.jp.debian.org/debian/ sid/main mime-support all 3.52-1 [35.5 kB]
+Get:11 http://ftp.jp.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.3~rc1-1 [1769 kB]
+Get:12 http://ftp.jp.debian.org/debian/ sid/main python2.7 amd64 2.7.3~rc1-1 [2718 kB]
+Get:13 http://ftp.jp.debian.org/debian/ sid/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:14 http://ftp.jp.debian.org/debian/ sid/main python all 2.7.2-10 [177 kB]
+Get:15 http://ftp.jp.debian.org/debian/ sid/main cdbs all 0.4.109 [79.4 kB]
+Get:16 http://ftp.jp.debian.org/debian/ sid/main debhelper all 9.20120312 [694 kB]
+Get:17 http://ftp.jp.debian.org/debian/ sid/main diffstat amd64 1.55-2 [29.9 kB]
+Get:18 http://ftp.jp.debian.org/debian/ sid/main quilt all 0.60-2 [377 kB]
+Get:19 http://ftp.jp.debian.org/debian/ sid/main zlib1g-dev amd64 1:1.2.6.dfsg-2 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 5163 kB in 1s (4153 kB/s)
+Fetched 12.0 MB in 2s (5638 kB/s)
Selecting previously unselected package libncursesw5.
-(Reading database ... 10814 files and directories currently installed.)
+(Reading database ... 10890 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_amd64.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_amd64.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_amd64.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_amd64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_amd64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_amd64.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_amd64.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_amd64.deb) ...
Selecting previously unselected package libunistring0.
@@ -125,27 +142,25 @@ Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_amd64.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_amd64.deb) ...
+Unpacking file (from .../archives/file_5.10-1_amd64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-3_amd64.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_amd64.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_amd64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_amd64.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_amd64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_amd64.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously unselected package gettext.
@@ -155,49 +170,49 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_amd64.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_amd64.deb) ...
Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-3) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -205,8 +220,8 @@ Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.8-2
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 libgpm2_1.20.4-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-4 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-11 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-8 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.10-1
+Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.10-1 groff-base_1.21-6 gzip_1.4-3 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 libgpm2_1.20.4-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libpng12-0_1.2.47-1 libpod-plainer-perl_1.03-1 libquadmath0_4.6.3-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.10-1 login_1:4.1.5-1 lsb-base_3.2+Debian31 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -216,10 +231,10 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bedtools_2.15.0-1.dsc)
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (bedtools_2.16.1-1.dsc)
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -237,7 +252,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-343774b6-6dca-4595-80cd-b14edd2af35d
+SCHROOT_SESSION_ID=sid-amd64-sbuild-1381889c-d61a-4c99-85bb-1dc3ce616ec9
SCHROOT_UID=31051
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -249,19 +264,33 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
+dpkg-buildpackage: source version 2.16.1-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bedtools-2.15.0
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
make[1]: Entering directory `/«PKGBUILDDIR»'
-Cleaning up.
+ * 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/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
@@ -275,14 +304,13 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- dpkg-source -b bedtools-2.15.0
+ dpkg-source -b bedtools-2.16.1
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: patches are not applied, applying them now
dpkg-source: info: applying gzstream.h.patch
-dpkg-source: info: building bedtools using existing ./bedtools_2.15.0.orig.tar.gz
-dpkg-source: warning: ignoring deletion of file src/utils/bedFile/bedFile.h.orig
-dpkg-source: info: building bedtools in bedtools_2.15.0-1.debian.tar.gz
-dpkg-source: info: building bedtools in bedtools_2.15.0-1.dsc
+dpkg-source: info: building bedtools using existing ./bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: building bedtools in bedtools_2.16.1-1.debian.tar.gz
+dpkg-source: info: building bedtools in bedtools_2.16.1-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
@@ -298,39 +326,31 @@ touch debian/stamp-patched
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
make[1]: Entering directory `/«PKGBUILDDIR»'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.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/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.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
@@ -369,148 +389,143 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * 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
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- 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]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- 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]
+ * 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]
-
- 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]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.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]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* 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]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * 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]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -519,47 +534,41 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
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]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* 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]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * 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.
@@ -571,7 +580,11 @@ DEB_MAKE_CHECK_TARGET unset, not running checks
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -579,6 +592,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -586,38 +605,110 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ 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»'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
+ rm -f debian/bedtools/DEBIAN/shlibs
rm /«PKGBUILDDIR»/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (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 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_amd64.deb'.
- dpkg-genchanges >../bedtools_2.15.0-1_amd64.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_amd64.deb'.
+ dpkg-genchanges >../bedtools_2.16.1-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-source: info: unapplying gzstream.h.patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-1514
+Build finished at 20120316-2038
Finished
────────
@@ -629,15 +720,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_amd64.changes:
+bedtools_2.16.1-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -645,45 +736,45 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
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- 65f70842da0b9fbe376819cc9110beb7139a3beb 394858 bedtools_2.15.0-1_amd64.deb
+ 6e98b4f157fc31357412d0e7c1a691f779a4d389 1089 bedtools_2.16.1-1.dsc
+ 79b634a26e2cf56669d05068954a328eb73e2942 977886 bedtools_2.16.1.orig.tar.gz
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- 8f19b6993b3e467e51b92f1496aac16f51cb206780a96d2adb7526bb8690aa20 394858 bedtools_2.15.0-1_amd64.deb
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+ 2cf489420b39b2d8fb6539a3b5b534cebd8383d2678094cb86fa891bdccf68d3 433932 bedtools_2.16.1-1_amd64.deb
Files:
- 446680ddaada61ec7246876042c9b459 1089 science optional bedtools_2.15.0-1.dsc
- c0cbcb748f54ed99fce47c687bd0f260 962861 science optional bedtools_2.15.0.orig.tar.gz
- 26766fd8ab3c709115cef6f5d28fb80f 4499 science optional bedtools_2.15.0-1.debian.tar.gz
- ca6f61f75be65643858e1b76599d9212 394858 science optional bedtools_2.15.0-1_amd64.deb
+ 82d49d758776f4866b29b99a122effda 1089 science optional bedtools_2.16.1-1.dsc
+ f9356528d6c70b2f25a91f0464a539f9 977886 science optional bedtools_2.16.1.orig.tar.gz
+ 5af58a135fb459c1e8513f7e9dc80d29 5035 science optional bedtools_2.16.1-1.debian.tar.gz
+ ddd0ee0ea1d713c064957da3f96944c4 433932 science optional bedtools_2.16.1-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_amd64.deb
+bedtools_2.16.1-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 394858 bytes: control archive= 1869 bytes.
+ size 433932 bytes: control archive= 1980 bytes.
865 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1268
+ Installed-Size: 1416
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -699,54 +790,58 @@ bedtools_2.15.0-1_amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/bin/
--rwxr-xr-x root/root 28 2012-01-11 15:14 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/bedToBam
--rwxr-xr-x root/root 34 2012-01-11 15:14 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/coverageBed
--rwxr-xr-x root/root 36 2012-01-11 15:14 ./usr/bin/windowMaker
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/bamToBed
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-01-11 15:14 ./usr/bin/tagBam
--rwxr-xr-x root/root 30 2012-01-11 15:14 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 32 2012-01-11 15:14 ./usr/bin/clusterBed
--rwxr-xr-x root/root 34 2012-01-11 15:14 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 34 2012-01-11 15:14 ./usr/bin/pairToBed
--rwxr-xr-x root/root 34 2012-01-11 15:14 ./usr/bin/intersectBed
--rwxr-xr-x root/root 35 2012-01-11 15:14 ./usr/bin/complementBed
--rwxr-xr-x root/root 28 2012-01-11 15:14 ./usr/bin/nucBed
--rwxr-xr-x root/root 32 2012-01-11 15:14 ./usr/bin/getOverlap
--rwxr-xr-x root/root 1237992 2012-01-11 15:14 ./usr/bin/bedtools
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 35 2012-01-11 15:14 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-01-11 15:14 ./usr/bin/annotateBed
--rwxr-xr-x root/root 35 2012-01-11 15:14 ./usr/bin/pairToPair
--rwxr-xr-x root/root 30 2012-01-11 15:14 ./usr/bin/linksBed
--rwxr-xr-x root/root 30 2012-01-11 15:14 ./usr/bin/flankBed
--rwxr-xr-x root/root 35 2012-01-11 15:14 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 29 2012-01-11 15:14 ./usr/bin/sortBed
--rwxr-xr-x root/root 29 2012-01-11 15:14 ./usr/bin/slopBed
--rwxr-xr-x root/root 34 2012-01-11 15:14 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 31 2012-01-11 15:14 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-01-11 15:14 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 32 2012-01-11 15:14 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-01-11 15:14 ./usr/bin/shuffleBed
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/share/
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-01-11 15:13 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2012-01-02 19:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2012-01-02 19:51 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-01-02 19:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2012-01-02 19:51 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-01-11 15:14 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2012-01-02 19:51 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11640 2012-01-02 19:51 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2012-01-05 10:53 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 832 2012-01-11 15:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/bin/
+-rwxr-xr-x root/root 28 2012-03-16 20:38 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 34 2012-03-16 20:38 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 36 2012-03-16 20:38 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 20:38 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-03-16 20:38 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 32 2012-03-16 20:38 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 34 2012-03-16 20:38 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 34 2012-03-16 20:38 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 34 2012-03-16 20:38 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 35 2012-03-16 20:38 ./usr/bin/complementBed
+-rwxr-xr-x root/root 31 2012-03-16 20:38 ./usr/bin/expandCols
+-rwxr-xr-x root/root 28 2012-03-16 20:38 ./usr/bin/nucBed
+-rwxr-xr-x root/root 32 2012-03-16 20:38 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 1388184 2012-03-16 20:38 ./usr/bin/bedtools
+-rwxr-xr-x root/root 31 2012-03-16 20:38 ./usr/bin/randomBed
+-rwxr-xr-x root/root 35 2012-03-16 20:38 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 28 2012-03-16 20:38 ./usr/bin/mapBed
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 35 2012-03-16 20:38 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 20:38 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 35 2012-03-16 20:38 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 30 2012-03-16 20:38 ./usr/bin/linksBed
+-rwxr-xr-x root/root 30 2012-03-16 20:38 ./usr/bin/flankBed
+-rwxr-xr-x root/root 35 2012-03-16 20:38 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 29 2012-03-16 20:38 ./usr/bin/sortBed
+-rwxr-xr-x root/root 29 2012-03-16 20:38 ./usr/bin/slopBed
+-rwxr-xr-x root/root 34 2012-03-16 20:38 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 31 2012-03-16 20:38 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 20:38 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 32 2012-03-16 20:38 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 20:38 ./usr/bin/shuffleBed
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 20:37 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-03-13 22:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-03-13 22:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 22:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-03-13 22:10 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 20:38 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 22:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-03-13 22:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4827 2012-03-16 13:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 934 2012-03-16 19:08 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -760,9 +855,9 @@ lintian
Subroutine IO::Socket::INET6::sockaddr_in6 redefined at /usr/share/perl/5.14/Exporter.pm line 67.
at /usr/share/perl5/IO/Socket/INET6.pm line 21
P: bedtools source: unneeded-build-dep-on-quilt
-P: bedtools source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5/
W: bedtools: binary-without-manpage usr/bin/annotateBed
W: bedtools: binary-without-manpage usr/bin/bamToBed
+W: bedtools: binary-without-manpage usr/bin/bamToFastq
W: bedtools: binary-without-manpage usr/bin/bed12ToBed6
W: bedtools: binary-without-manpage usr/bin/bedToBam
W: bedtools: binary-without-manpage usr/bin/bedToIgv
@@ -772,12 +867,14 @@ W: bedtools: binary-without-manpage usr/bin/closestBed
W: bedtools: binary-without-manpage usr/bin/clusterBed
W: bedtools: binary-without-manpage usr/bin/complementBed
W: bedtools: binary-without-manpage usr/bin/coverageBed
+W: bedtools: binary-without-manpage usr/bin/expandCols
W: bedtools: binary-without-manpage usr/bin/fastaFromBed
W: bedtools: binary-without-manpage usr/bin/flankBed
W: bedtools: binary-without-manpage usr/bin/genomeCoverageBed
W: bedtools: binary-without-manpage usr/bin/getOverlap
W: bedtools: binary-without-manpage usr/bin/intersectBed
W: bedtools: binary-without-manpage usr/bin/linksBed
+W: bedtools: binary-without-manpage usr/bin/mapBed
W: bedtools: binary-without-manpage usr/bin/maskFastaFromBed
W: bedtools: binary-without-manpage usr/bin/mergeBed
W: bedtools: binary-without-manpage usr/bin/multiBamCov
@@ -785,6 +882,7 @@ W: bedtools: binary-without-manpage usr/bin/multiIntersectBed
W: bedtools: binary-without-manpage usr/bin/nucBed
W: bedtools: binary-without-manpage usr/bin/pairToBed
W: bedtools: binary-without-manpage usr/bin/pairToPair
+W: bedtools: binary-without-manpage usr/bin/randomBed
W: bedtools: binary-without-manpage usr/bin/shuffleBed
W: bedtools: binary-without-manpage usr/bin/slopBed
W: bedtools: binary-without-manpage usr/bin/sortBed
@@ -812,18 +910,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 100880
-Build-Time: 83
+Build-Space: 117600
+Build-Time: 106
Distribution: unstable
-Install-Time: 28
-Job: bedtools_2.15.0-1.dsc
+Install-Time: 15
+Job: bedtools_2.16.1-1.dsc
Lintian: pass
Package: bedtools
-Package-Time: 117
-Source-Version: 2.15.0-1
-Space: 100880
+Package-Time: 124
+Source-Version: 2.16.1-1
+Space: 117600
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-1514
-Build needed 00:01:57, 100880k disc space
+Finished at 20120316-2038
+Build needed 00:02:04, 117600k disc space
diff --git a/dsc b/dsc
index 11960ad..a95886f 100644
--- a/dsc
+++ b/dsc
@@ -5,41 +5,41 @@ Format: 3.0 (quilt)
Source: bedtools
Binary: bedtools
Architecture: any
-Version: 2.15.0-1
+Version: 2.16.1-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
Homepage: http://code.google.com/p/bedtools/
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
Vcs-Browser: http://git.debian.org/?p=debian-med/bedtools.git
Vcs-Git: git://git.debian.org/git/debian-med/bedtools.git
Build-Depends: cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Package-List:
bedtools deb science optional
Checksums-Sha1:
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- d865eee05d8abe20118552c8e48581b648f2dd8d 4499 bedtools_2.15.0-1.debian.tar.gz
+ 79b634a26e2cf56669d05068954a328eb73e2942 977886 bedtools_2.16.1.orig.tar.gz
+ e4f81f729a5ebaafe2855fd22a2e5814db725e35 5035 bedtools_2.16.1-1.debian.tar.gz
Checksums-Sha256:
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+ 6f6667d59719388d01c2c2dd51050998f6bef3e074b43a53df09b99dbe6cac6b 977886 bedtools_2.16.1.orig.tar.gz
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diff --git a/upload b/upload
new file mode 100644
index 0000000..1d63846
--- /dev/null
+++ b/upload
@@ -0,0 +1,6 @@
+u bedtools_2.16.1-1.dsc ftp.upload.debian.org Fri Mar 16 20:43:24 2012
+u bedtools_2.16.1.orig.tar.gz ftp.upload.debian.org Fri Mar 16 20:43:27 2012
+u bedtools_2.16.1-1_amd64.deb ftp.upload.debian.org Fri Mar 16 20:43:30 2012
+u bedtools_2.16.1-1.debian.tar.gz ftp.upload.debian.org Fri Mar 16 20:43:31 2012
+u bedtools_2.16.1-1_amd64.changes ftp.upload.debian.org Fri Mar 16 20:43:32 2012
+s bedtools_2.16.1-1_amd64.changes ftp.upload.debian.org Fri Mar 16 20:43:32 2012
--
Suite of utilities for comparing genomic features.
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