[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.12.0-1-3-gd4672d3
Charles Plessy
plessy at debian.org
Sat Sep 24 02:43:42 UTC 2011
The following commit has been merged in the meta branch:
commit d4672d37ae58d679dd7ed13511628d3c7a61c409
Author: Charles Plessy <plessy at debian.org>
Date: Sat Sep 24 11:40:55 2011 +0900
Built 2.13.2-1.
diff --git a/amd64.changes b/amd64.changes
index e33f1f8..df342c8 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Sat, 10 Sep 2011 23:32:43 +0900
+Date: Sat, 24 Sep 2011 09:34:29 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.13.1-1
+Version: 2.13.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,44 +14,39 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.1-1) unstable; urgency=low
+ bedtools (2.13.2-1) unstable; urgency=low
.
- [2e3fe5e] New upstream release.
- [ff5450e] Compress source and binary packages with xz.
- [ef58a33] Suggest filo for the groupBy command.
- [df206c0] Mangle debian/watch download URL.
- [2fe7cff] Simplified repacking as upstream tarballs do not contain
- ‘*/*DS_Store’ files anymore.
+ [1930a26] New upstream release.
Checksums-Sha1:
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- 4e891972a2f1a6cf41697826c6c23f6feb3a5be2 658236 bedtools_2.13.1.orig.tar.xz
- 50185fee6dd5960fbcec46291870cae35c8860b5 4254 bedtools_2.13.1-1.debian.tar.gz
- 2c6c4d5b1a1caaf8473fddda2b5c02a15eafeab2 647786 bedtools_2.13.1-1_amd64.deb
+ 46ff4b743bad81eafebd2b5b9302b3fe3edd3c78 1967 bedtools_2.13.2-1.dsc
+ ab0742042fb5b01ec7b54a19402077b017c1a3cc 659356 bedtools_2.13.2.orig.tar.xz
+ e590bfac6fb078834cae5f1dd79fcb12ddda6c4d 4285 bedtools_2.13.2-1.debian.tar.gz
+ 6ee8a0c749e9f76251b255ce08219da9eeed53af 665800 bedtools_2.13.2-1_amd64.deb
Checksums-Sha256:
- 0ce17a73e50a3eb1ec6938a4794f7918c0504c8f37b7f970d5f28548158f4273 1921 bedtools_2.13.1-1.dsc
- 3a7d2fd9d897d51110630597c9218f718cac937984507eb88a96654ca4c5a625 658236 bedtools_2.13.1.orig.tar.xz
- 173c10611370d080f4f69470adfacade3a7d01ecc7c502374536b4637132c2bd 4254 bedtools_2.13.1-1.debian.tar.gz
- 832e7d1b57e31721883b787563329ffca7cc973d0e5e5cae6df574c9d2bceb81 647786 bedtools_2.13.1-1_amd64.deb
+ 7e2dc635375c31e7837d63e0635a6ddb412cfcce7755e2ddf5a9b123b2f0997d 1967 bedtools_2.13.2-1.dsc
+ 51895a7c33c6fab280a7a4b872f44225848f827d9abb496499bd05232a0b2aae 659356 bedtools_2.13.2.orig.tar.xz
+ e0081a522c13afe9d73d3b1419848519dd0d21dbe2043f113046edc8a89e426d 4285 bedtools_2.13.2-1.debian.tar.gz
+ 4e53cd359fc3b3d279ca0f1c13eb49689fd3d85e2a945286e91b50672e355ce8 665800 bedtools_2.13.2-1_amd64.deb
Files:
- 4cf7e7e23566d073fe75a1e04e611e49 1921 science optional bedtools_2.13.1-1.dsc
- 2f4be77ca3e394b6b277edefaeee32da 658236 science optional bedtools_2.13.1.orig.tar.xz
- bf798ce7e51f34e08e402f46c6243476 4254 science optional bedtools_2.13.1-1.debian.tar.gz
- d1d8f9c3b62d01970bd39289a6665a76 647786 science optional bedtools_2.13.1-1_amd64.deb
+ f40d3a275c0ded72a21fa6afc98c1c73 1967 science optional bedtools_2.13.2-1.dsc
+ 9e3485e2208dedb012c81e6c2921ec6c 659356 science optional bedtools_2.13.2.orig.tar.xz
+ 38070fd20606966c2a458bf5c6528612 4285 science optional bedtools_2.13.2-1.debian.tar.gz
+ 81dc4b2a68d23e1b009dc0ed258724e0 665800 science optional bedtools_2.13.2-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 31a66a4..bbc6740 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,18 +1,18 @@
sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.1-1 (amd64) 11 sept. 2011 09:42 ║
+║ bedtools 2.13.2-1 (amd64) 24 sept. 2011 10:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.1-1
-Source Version: 2.13.1-1
+Version: 2.13.2-1
+Source Version: 2.13.2-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bedtools-bd3uUV/bedtools-2.13.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-bd3uUV' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-3ad58e5c-083f-4671-aa1c-6810b3375dc4' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bedtools-JPzpUG/bedtools-2.13.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-JPzpUG' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-af2cb0e8-6bb7-48b3-969c-16faabdbe081' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -37,14 +37,14 @@ Reading state information...
Local sources
─────────────
-bedtools_2.13.1-1.dsc exists in .; copying to chroot
+bedtools_2.13.2-1.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-YJEiaO/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-_lBGjF/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -60,15 +60,15 @@ The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/714 B of archives.
+Need to get 0 B/716 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10819 files and directories currently installed.)
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ... 10726 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
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, 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, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-ebcjhq/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-uGbK9b/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
OK
Reading package lists...
@@ -97,52 +97,52 @@ The following NEW packages will be installed:
sbuild-build-depends-bedtools-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9848 kB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10819 files and directories currently installed.)
+Need to get 0 B/9842 kB of archives.
+After this operation, 29.0 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10726 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.08-1_amd64.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
-Selecting previously deselected package sbuild-build-depends-bedtools-dummy.
+Selecting previously unselected package sbuild-build-depends-bedtools-dummy.
Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -156,6 +156,7 @@ Setting up libmagic1 (5.08-1) ...
Setting up file (5.08-1) ...
Setting up gettext-base (0.18.1.1-4) ...
Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up cdbs (0.4.99) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -164,10 +165,9 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.6) ...
-Setting up cdbs (0.4.96) ...
+Setting up debhelper (8.9.7) ...
Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-7) ...
+Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
@@ -176,8 +176,8 @@ Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.1-10 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-4
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-16-1 e2fsprogs_1.42~WIP-2011-09-16-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-09-16-1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.1-11 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.1-11 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-16-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -187,13 +187,10 @@ Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Sep 11 00:37:21 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.1
-dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (bedtools_2.13.2-1.dsc)
+dpkg-source: info: extracting bedtools in bedtools-2.13.2
+dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -211,7 +208,7 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-3ad58e5c-083f-4671-aa1c-6810b3375dc4
+SCHROOT_SESSION_ID=sid-amd64-sbuild-af2cb0e8-6bb7-48b3-969c-16faabdbe081
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -222,21 +219,21 @@ USERNAME=charles
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.1-1
+dpkg-buildpackage: source version 2.13.2-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bedtools-2.13.1
+ dpkg-source --before-build bedtools-2.13.2
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
make[1]: Entering directory `/«PKGBUILDDIR»'
Cleaning up.
make[1]: Leaving directory `/«PKGBUILDDIR»'
@@ -254,14 +251,14 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- dpkg-source -b bedtools-2.13.1
+ dpkg-source -b bedtools-2.13.2
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override)
+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_2.13.1.orig.tar.xz
+dpkg-source: info: building bedtools using existing ./bedtools_2.13.2.orig.tar.xz
dpkg-source: warning: ignoring deletion of file src/utils/bedFile/bedFile.h.orig
-dpkg-source: info: building bedtools in bedtools_2.13.1-1.debian.tar.gz
-dpkg-source: info: building bedtools in bedtools_2.13.1-1.dsc
+dpkg-source: info: building bedtools in bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: info: building bedtools in bedtools_2.13.2-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
@@ -277,7 +274,7 @@ 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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
make[1]: Entering directory `/«PKGBUILDDIR»'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
@@ -292,13 +289,11 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/genomeFile
- * compiling genomeFile.cpp
-genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
-genomeFile.cpp:51:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+- Building in src/utils/chromsweep
+ * compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -358,8 +353,17 @@ 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]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.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 main(int, char**)':
@@ -464,9 +468,9 @@ pairToBedMain.cpp: In function 'int 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:254:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:255:12: 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:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -567,13 +571,14 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_amd64.deb'.
- dpkg-genchanges >../bedtools_2.13.1-1_amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_amd64.deb'.
+ dpkg-genchanges >../bedtools_2.13.2-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build bedtools-2.13.1
+ dpkg-source --after-build bedtools-2.13.2
+dpkg-source: info: unapplying gzstream.h.patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110911-0944
+Build finished at 20110924-1031
Finished
────────
@@ -585,15 +590,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.1-1_amd64.changes:
+bedtools_2.13.2-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Sat, 10 Sep 2011 23:32:43 +0900
+Date: Sat, 24 Sep 2011 09:34:29 +0900
Source: bedtools
Binary: bedtools
Architecture: source amd64
-Version: 2.13.1-1
+Version: 2.13.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -601,48 +606,43 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.1-1) unstable; urgency=low
+ bedtools (2.13.2-1) unstable; urgency=low
.
- [2e3fe5e] New upstream release.
- [ff5450e] Compress source and binary packages with xz.
- [ef58a33] Suggest filo for the groupBy command.
- [df206c0] Mangle debian/watch download URL.
- [2fe7cff] Simplified repacking as upstream tarballs do not contain
- ‘*/*DS_Store’ files anymore.
+ [1930a26] New upstream release.
Checksums-Sha1:
- b9f5b37f0bd8f1f0afb7611d53a893a3398ee77a 1035 bedtools_2.13.1-1.dsc
- 4e891972a2f1a6cf41697826c6c23f6feb3a5be2 658236 bedtools_2.13.1.orig.tar.xz
- 50185fee6dd5960fbcec46291870cae35c8860b5 4254 bedtools_2.13.1-1.debian.tar.gz
- 2c6c4d5b1a1caaf8473fddda2b5c02a15eafeab2 647786 bedtools_2.13.1-1_amd64.deb
+ 7c37cff1c61f7a14e8c143274ae8a0c411fa4e2c 1081 bedtools_2.13.2-1.dsc
+ ab0742042fb5b01ec7b54a19402077b017c1a3cc 659356 bedtools_2.13.2.orig.tar.xz
+ e590bfac6fb078834cae5f1dd79fcb12ddda6c4d 4285 bedtools_2.13.2-1.debian.tar.gz
+ 6ee8a0c749e9f76251b255ce08219da9eeed53af 665800 bedtools_2.13.2-1_amd64.deb
Checksums-Sha256:
- f5278a03bbbe6479b7fbec7983689e99a4a19dbb6858ad80207a7b33f6453efb 1035 bedtools_2.13.1-1.dsc
- 3a7d2fd9d897d51110630597c9218f718cac937984507eb88a96654ca4c5a625 658236 bedtools_2.13.1.orig.tar.xz
- 173c10611370d080f4f69470adfacade3a7d01ecc7c502374536b4637132c2bd 4254 bedtools_2.13.1-1.debian.tar.gz
- 832e7d1b57e31721883b787563329ffca7cc973d0e5e5cae6df574c9d2bceb81 647786 bedtools_2.13.1-1_amd64.deb
+ 0549ad48af5afcc99bcbb17d9bd89ae1f0a911c821454cd21946d95278f5d734 1081 bedtools_2.13.2-1.dsc
+ 51895a7c33c6fab280a7a4b872f44225848f827d9abb496499bd05232a0b2aae 659356 bedtools_2.13.2.orig.tar.xz
+ e0081a522c13afe9d73d3b1419848519dd0d21dbe2043f113046edc8a89e426d 4285 bedtools_2.13.2-1.debian.tar.gz
+ 4e53cd359fc3b3d279ca0f1c13eb49689fd3d85e2a945286e91b50672e355ce8 665800 bedtools_2.13.2-1_amd64.deb
Files:
- 83996fe2636f38a927ece15a3e48ca7c 1035 science optional bedtools_2.13.1-1.dsc
- 2f4be77ca3e394b6b277edefaeee32da 658236 science optional bedtools_2.13.1.orig.tar.xz
- bf798ce7e51f34e08e402f46c6243476 4254 science optional bedtools_2.13.1-1.debian.tar.gz
- d1d8f9c3b62d01970bd39289a6665a76 647786 science optional bedtools_2.13.1-1_amd64.deb
+ 66832e788feba231011e3c6beb1b265b 1081 science optional bedtools_2.13.2-1.dsc
+ 9e3485e2208dedb012c81e6c2921ec6c 659356 science optional bedtools_2.13.2.orig.tar.xz
+ 38070fd20606966c2a458bf5c6528612 4285 science optional bedtools_2.13.2-1.debian.tar.gz
+ 81dc4b2a68d23e1b009dc0ed258724e0 665800 science optional bedtools_2.13.2-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.1-1_amd64.deb
+bedtools_2.13.2-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 647786 bytes: control archive= 1721 bytes.
- 837 bytes, 18 lines control
- 2028 bytes, 35 lines md5sums
+ size 665800 bytes: control archive= 1715 bytes.
+ 835 bytes, 18 lines control
+ 2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.1-1
+ Version: 2.13.2-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4772
- Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4691
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -656,49 +656,49 @@ bedtools_2.13.1-1_amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-11 09:42 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 586 2011-09-07 09:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-07 09:36 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-07 09:36 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-07 09:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1586 2011-09-07 09:36 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 4611 2011-09-10 23:21 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 10990 2011-09-07 09:36 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 391 2011-09-10 23:32 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-11 09:44 ./usr/bin/
--rwxr-xr-x root/root 147088 2011-09-11 09:44 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 180192 2011-09-11 09:44 ./usr/bin/pairToPair
--rwxr-xr-x root/root 272656 2011-09-11 09:44 ./usr/bin/coverageBed
--rwxr-xr-x root/root 226552 2011-09-11 09:44 ./usr/bin/bedToBam
--rwxr-xr-x root/root 93640 2011-09-11 09:44 ./usr/bin/overlap
--rwxr-xr-x root/root 110016 2011-09-11 09:44 ./usr/bin/linksBed
--rwxr-xr-x root/root 114088 2011-09-11 09:44 ./usr/bin/mergeBed
--rwxr-xr-x root/root 110112 2011-09-11 09:44 ./usr/bin/complementBed
--rwxr-xr-x root/root 147112 2011-09-11 09:44 ./usr/bin/nucBed
--rwxr-xr-x root/root 118224 2011-09-11 09:44 ./usr/bin/flankBed
--rwxr-xr-x root/root 264432 2011-09-11 09:44 ./usr/bin/tagBam
--rwxr-xr-x root/root 294856 2011-09-11 09:44 ./usr/bin/intersectBed
--rwxr-xr-x root/root 115160 2011-09-11 09:44 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 110032 2011-09-11 09:44 ./usr/bin/slopBed
--rwxr-xr-x root/root 109976 2011-09-11 09:44 ./usr/bin/annotateBed
--rwxr-xr-x root/root 118168 2011-09-11 09:44 ./usr/bin/subtractBed
--rwxr-xr-x root/root 134672 2011-09-11 09:44 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 278456 2011-09-11 09:44 ./usr/bin/windowBed
--rwxr-xr-x root/root 148008 2011-09-11 09:44 ./usr/bin/sortBed
--rwxr-xr-x root/root 101832 2011-09-11 09:44 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 126376 2011-09-11 09:44 ./usr/bin/closestBed
--rwxr-xr-x root/root 214784 2011-09-11 09:44 ./usr/bin/bamToBed
--rwxr-xr-x root/root 356328 2011-09-11 09:44 ./usr/bin/pairToBed
--rwxr-xr-x root/root 288936 2011-09-11 09:44 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 65024 2011-09-11 09:44 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 126456 2011-09-11 09:44 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 291896 2011-09-11 09:44 ./usr/bin/multiBamCov
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-24 10:28 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-09-24 00:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-24 00:57 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-24 00:57 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-24 00:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-09-24 00:57 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-09-24 09:33 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11135 2011-09-24 00:57 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 417 2011-09-24 09:36 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-24 10:30 ./usr/bin/
+-rwxr-xr-x root/root 147112 2011-09-24 10:30 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 180008 2011-09-24 10:30 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 274368 2011-09-24 10:30 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 229232 2011-09-24 10:30 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 93664 2011-09-24 10:30 ./usr/bin/overlap
+-rwxr-xr-x root/root 110040 2011-09-24 10:30 ./usr/bin/linksBed
+-rwxr-xr-x root/root 114112 2011-09-24 10:30 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 114168 2011-09-24 10:30 ./usr/bin/complementBed
+-rwxr-xr-x root/root 147136 2011-09-24 10:30 ./usr/bin/nucBed
+-rwxr-xr-x root/root 119096 2011-09-24 10:30 ./usr/bin/flankBed
+-rwxr-xr-x root/root 267976 2011-09-24 10:30 ./usr/bin/tagBam
+-rwxr-xr-x root/root 346392 2011-09-24 10:30 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 118328 2011-09-24 10:30 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 110112 2011-09-24 10:30 ./usr/bin/slopBed
+-rwxr-xr-x root/root 110000 2011-09-24 10:30 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 118192 2011-09-24 10:30 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 135456 2011-09-24 10:30 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 279144 2011-09-24 10:30 ./usr/bin/windowBed
+-rwxr-xr-x root/root 150952 2011-09-24 10:30 ./usr/bin/sortBed
+-rwxr-xr-x root/root 101856 2011-09-24 10:30 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 126400 2011-09-24 10:30 ./usr/bin/closestBed
+-rwxr-xr-x root/root 215928 2011-09-24 10:30 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 357120 2011-09-24 10:30 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 291184 2011-09-24 10:30 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 65032 2011-09-24 10:30 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 126480 2011-09-24 10:30 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 294864 2011-09-24 10:30 ./usr/bin/multiBamCov
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -779,17 +779,17 @@ The following packages will be REMOVED:
sbuild-build-depends-bedtools-dummy* sbuild-build-depends-core-dummy*
zlib1g-dev*
0 upgraded, 0 newly installed, 23 to remove and 0 not upgraded.
-After this operation, 29.1 MB disk space will be freed.
-(Reading database ... 12295 files and directories currently installed.)
+After this operation, 29.0 MB disk space will be freed.
+(Reading database ... 12208 files and directories currently installed.)
Removing sbuild-build-depends-bedtools-dummy ...
-Removing cdbs ...
+Removing quilt ...
+Purging configuration files for quilt ...
Removing debhelper ...
Removing man-db ...
Purging configuration files for man-db ...
Removing bsdmainutils ...
Purging configuration files for bsdmainutils ...
-Removing quilt ...
-Purging configuration files for quilt ...
+Removing cdbs ...
Removing diffstat ...
Removing file ...
Removing po-debconf ...
@@ -822,18 +822,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 131372
-Build-Time: 134
+Build-Space: 135620
+Build-Time: 145
Distribution: unstable
Install-Time: 9
-Job: bedtools_2.13.1-1.dsc
+Job: bedtools_2.13.2-1.dsc
Lintian: pass
Package: bedtools
-Package-Time: 146
-Source-Version: 2.13.1-1
-Space: 131372
+Package-Time: 160
+Source-Version: 2.13.2-1
+Space: 135620
Status: successful
-Version: 2.13.1-1
+Version: 2.13.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110911-0944
-Build needed 00:02:26, 131372k disc space
+Finished at 20110924-1031
+Build needed 00:02:40, 135620k disc space
diff --git a/dsc b/dsc
index 17714a0..3c936b4 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: bedtools
Binary: bedtools
Architecture: any
-Version: 2.13.1-1
+Version: 2.13.2-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -14,30 +14,32 @@ Standards-Version: 3.9.2
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, zlib1g-dev
+Package-List:
+ bedtools deb science optional
Checksums-Sha1:
- 4e891972a2f1a6cf41697826c6c23f6feb3a5be2 658236 bedtools_2.13.1.orig.tar.xz
- 50185fee6dd5960fbcec46291870cae35c8860b5 4254 bedtools_2.13.1-1.debian.tar.gz
+ ab0742042fb5b01ec7b54a19402077b017c1a3cc 659356 bedtools_2.13.2.orig.tar.xz
+ e590bfac6fb078834cae5f1dd79fcb12ddda6c4d 4285 bedtools_2.13.2-1.debian.tar.gz
Checksums-Sha256:
- 3a7d2fd9d897d51110630597c9218f718cac937984507eb88a96654ca4c5a625 658236 bedtools_2.13.1.orig.tar.xz
- 173c10611370d080f4f69470adfacade3a7d01ecc7c502374536b4637132c2bd 4254 bedtools_2.13.1-1.debian.tar.gz
+ 51895a7c33c6fab280a7a4b872f44225848f827d9abb496499bd05232a0b2aae 659356 bedtools_2.13.2.orig.tar.xz
+ e0081a522c13afe9d73d3b1419848519dd0d21dbe2043f113046edc8a89e426d 4285 bedtools_2.13.2-1.debian.tar.gz
Files:
- 2f4be77ca3e394b6b277edefaeee32da 658236 bedtools_2.13.1.orig.tar.xz
- bf798ce7e51f34e08e402f46c6243476 4254 bedtools_2.13.1-1.debian.tar.gz
+ 9e3485e2208dedb012c81e6c2921ec6c 659356 bedtools_2.13.2.orig.tar.xz
+ 38070fd20606966c2a458bf5c6528612 4285 bedtools_2.13.2-1.debian.tar.gz
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--
Suite of utilities for comparing genomic features.
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