[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.16.1-1-2-gd3cbc06
Charles Plessy
plessy at debian.org
Mon Nov 5 05:13:30 UTC 2012
The following commit has been merged in the meta branch:
commit d3cbc06281881ba4375ca68af5f46a4f16ebcaf5
Author: Charles Plessy <plessy at debian.org>
Date: Mon Nov 5 14:10:53 2012 +0900
Build logs for 2.17.0-1.
diff --git a/armel.log b/armel.log
index 76ac3c9..26b9c97 100644
--- a/armel.log
+++ b/armel.log
@@ -1,4 +1,4 @@
-From buildd at alwyn.debian.org Fri Mar 16 12:54:47 2012
+From buildd at alwyn.debian.org Sun Nov 04 12:02:01 2012
Return-path: <buildd at alwyn.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,23 +6,23 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
- id 1S8WgB-0002eu-3F
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:54:47 +0000
+ id 1TUytt-0005UK-BH
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 12:02:01 +0000
Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
- id 1S8WgA-0007mi-66
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:54:46 +0000
+ id 1TUyts-0007Wv-47
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 12:02:00 +0000
Received: from buildd by alwyn.debian.org with local (Exim 4.72)
(envelope-from <buildd at alwyn.debian.org>)
- id 1S8Wg8-0003QC-MV; Fri, 16 Mar 2012 12:54:44 +0000
-Date: Fri, 16 Mar 2012 12:54:44 +0000
-Message-Id: <E1S8Wg8-0003QC-MV at alwyn.debian.org>
+ id 1TUytq-0007Gc-7q; Sun, 04 Nov 2012 12:01:58 +0000
+Date: Sun, 04 Nov 2012 12:01:58 +0000
+Message-Id: <E1TUytq-0007Gc-7q at alwyn.debian.org>
From: buildd on alwyn <buildd at alwyn.debian.org>
To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on armel (dist=sid)
+Subject: Log for successful build of bedtools_2.17.0-1 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,40 +30,31 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alwyn.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (armel) 16 Mar 2012 12:21 ║
+║ bedtools 2.17.0-1 (armel) 04 Nov 2012 11:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: armel
-Get:1 http://ftp.uk.debian.org unstable InRelease [198 kB]
-Get:2 http://incoming.debian.org unstable InRelease [198 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6213 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [219 kB]
+Get:2 http://incoming.debian.org unstable InRelease [219 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6381 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.8 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armel Packages [5770 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib armel Packages [36.9 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2223 B]
-Get:11 http://ftp.uk.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:12 http://ftp.uk.debian.org unstable/main Translation-en [3902 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main armel Packages [5770 kB]
-Get:16 http://incoming.debian.org unstable/contrib armel Packages [36.9 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [59.8 kB]
-Get:22 http://incoming.debian.org Packages [692 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.4 MB in 1min 19s (421 kB/s)
+Get:5 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.1 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [6040 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main armel Packages [6040 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [36.9 kB]
+Get:13 http://incoming.debian.org unstable/contrib armel Packages [36.9 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.8 MB in 1min 36s (269 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,12 +74,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (858 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (779 kB/s)
Download complete and in download only mode
Check arch
@@ -102,58 +93,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-7)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -164,10 +155,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -177,165 +168,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 48 not upgraded.
-Need to get 17.0 MB of archives.
-After this operation, 46.4 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main zlib1g armel 1:1.2.6.dfsg-2 [85.4 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armel 5.9-4 [303 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.1-1 [34.9 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armel 1.0.0h-1 [1013 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.10-1 [250 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.30.2-6 [1744 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-7 [818 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.4-2 [140 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armel 2.0.1-7.2 [114 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armel 4.8.30-11 [622 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.1 [208 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.1-1 [1030 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.10-1 [52.7 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armel 3.7.10-1 [400 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armel 2.7.3~rc1-1 [1660 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armel 2.7.3~rc1-1 [2696 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 45 not upgraded.
+Need to get 16.2 MB of archives.
+After this operation, 45.1 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armel 5.9-10 [120 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.2-1 [35.1 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armel 1.0.1c-4 [1074 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armel 0.18.1.1-9 [26.4 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.11-2 [200 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.31-1 [247 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armel 3.7.14.1-1 [419 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-6 [826 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.33.12+really2.32.4-3 [1694 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.6-1 [120 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armel 2.1.0-1 [116 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armel 0.18.1.1-9 [132 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.3 [208 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-9 [1079 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.3-1 [1025 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.11-2 [51.4 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-9 [138 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armel 2.7.3-5 [1675 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armel 2.7.3-5 [2718 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
Get:26 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-9 [1888 kB]
Get:28 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:29 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-2 [28.5 kB]
+Get:30 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-3 [28.6 kB]
Get:32 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.6.dfsg-2 [209 kB]
+Get:33 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.0 MB in 4s (3539 kB/s)
-(Reading database ... 10578 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_armel.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10578 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_armel.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_armel.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_armel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_armel.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_armel.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_armel.deb) ...
-Selecting previously unselected package libxml2.
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+Fetched 16.2 MB in 8s (1990 kB/s)
+Selecting previously unselected package libncursesw5:armel.
+(Reading database ... 10649 files and directories currently installed.)
+Unpacking libncursesw5:armel (from .../libncursesw5_5.9-10_armel.deb) ...
+Selecting previously unselected package libpipeline1:armel.
+Unpacking libpipeline1:armel (from .../libpipeline1_1.2.2-1_armel.deb) ...
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+Unpacking libssl1.0.0:armel (from .../libssl1.0.0_1.0.1c-4_armel.deb) ...
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+Unpacking libmagic1:armel (from .../libmagic1_5.11-2_armel.deb) ...
+Selecting previously unselected package libpcre3:armel.
+Unpacking libpcre3:armel (from .../libpcre3_1%3a8.31-1_armel.deb) ...
+Selecting previously unselected package libsqlite3-0:armel.
+Unpacking libsqlite3-0:armel (from .../libsqlite3-0_3.7.14.1-1_armel.deb) ...
+Selecting previously unselected package libxml2:armel.
+Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-6_armel.deb) ...
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+Unpacking libglib2.0-0:armel (from .../libglib2.0-0_2.33.12+really2.32.4-3_armel.deb) ...
+Selecting previously unselected package libcroco3:armel.
+Unpacking libcroco3:armel (from .../libcroco3_0.6.6-1_armel.deb) ...
+Selecting previously unselected package libexpat1:armel.
+Unpacking libexpat1:armel (from .../libexpat1_2.1.0-1_armel.deb) ...
+Selecting previously unselected package libunistring0:armel.
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Selecting previously unselected package python.
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-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:armel.
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+Setting up libncursesw5:armel (5.9-10) ...
+Setting up libpipeline1:armel (1.2.2-1) ...
+Setting up libssl1.0.0:armel (1.0.1c-4) ...
+Setting up libasprintf0c2:armel (0.18.1.1-9) ...
+Setting up libmagic1:armel (5.11-2) ...
+Setting up libpcre3:armel (1:8.31-1) ...
+Setting up libsqlite3-0:armel (3.7.14.1-1) ...
+Setting up libxml2:armel (2.8.0+dfsg1-6) ...
+Setting up libffi5:armel (3.0.10-3) ...
+Setting up libglib2.0-0:armel (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:armel (0.6.6-1) ...
+Setting up libexpat1:armel (2.1.0-1) ...
+Setting up libunistring0:armel (0.9.3-5) ...
+Setting up libgettextpo0:armel (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:armel (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.2-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 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_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 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_3.10 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_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 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_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgomp1_4.6.2-12 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 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 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 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_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.2-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-2 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -346,12 +335,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -362,18 +351,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture armel
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -389,11 +378,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -401,30 +390,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -435,7 +426,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -510,7 +501,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -519,7 +510,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -569,10 +560,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -595,6 +589,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -638,7 +633,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -662,7 +657,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -676,6 +671,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -749,16 +745,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0'
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
@@ -774,39 +792,42 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-armel-z49NH1/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org> >../bedtools_2.16.1-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org> >../bedtools_2.17.0-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1254
+Build finished at 20121104-1201
-bedtools_2.16.1-1_armel.changes:
+bedtools_2.17.0-1_armel.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: armel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org>
@@ -814,38 +835,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 89b66d65305953d366019ae678a1e1c41bb82185 366444 bedtools_2.16.1-1_armel.deb
+ 1e446ef69cef4430e63b201d1d801c4e513d3170 383128 bedtools_2.17.0-1_armel.deb
Checksums-Sha256:
- eec185a1183a74a23e74057d503c3377263eb192e2206b0b19078e3f9f9f773b 366444 bedtools_2.16.1-1_armel.deb
+ d50b46feb8485155e938fd057d9c49504070b91e9385d7805e3638e86e5c2a10 383128 bedtools_2.17.0-1_armel.deb
Files:
- 10445aad88a29b4a3c0401a89cdf7e70 366444 science optional bedtools_2.16.1-1_armel.deb
+ fcc2a53539386c4754217b404641bdc3 383128 science optional bedtools_2.17.0-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_armel.deb
+bedtools_2.17.0-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 366444 bytes: control archive= 1976 bytes.
- 865 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 383128 bytes: control archive= 4107 bytes.
+ 32 bytes, 1 lines conffiles
+ 833 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1206
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1368
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -859,58 +884,168 @@ bedtools_2.16.1-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/annotateBed
--rwxr-xr-x root/root 29 2012-03-16 12:53 ./usr/bin/sortBed
--rwxr-xr-x root/root 36 2012-03-16 12:53 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 31 2012-03-16 12:53 ./usr/bin/windowBed
--rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 31 2012-03-16 12:53 ./usr/bin/randomBed
--rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/complementBed
--rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/pairToBed
--rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/nucBed
--rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/flankBed
--rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/closestBed
--rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/mergeBed
--rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/intersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/tagBam
--rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/mapBed
--rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/pairToPair
--rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/bedpeToBam
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+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
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+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
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+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
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+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
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+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
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+-rwxr-xr-x root/root 37 2012-11-04 12:01 ./usr/bin/sortBed
+-rwxr-xr-x root/root 44 2012-11-04 12:01 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 39 2012-11-04 12:01 ./usr/bin/windowBed
+-rwxr-xr-x root/root 40 2012-11-04 12:01 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 39 2012-11-04 12:01 ./usr/bin/randomBed
+-rwxr-xr-x root/root 43 2012-11-04 12:01 ./usr/bin/complementBed
+-rwxr-xr-x root/root 38 2012-11-04 12:01 ./usr/bin/linksBed
+-rwxr-xr-x root/root 42 2012-11-04 12:01 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 36 2012-11-04 12:01 ./usr/bin/nucBed
+-rwxr-xr-x root/root 43 2012-11-04 12:01 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 38 2012-11-04 12:01 ./usr/bin/flankBed
+-rwxr-xr-x root/root 40 2012-11-04 12:01 ./usr/bin/closestBed
+-rwxr-xr-x root/root 38 2012-11-04 12:01 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 42 2012-11-04 12:01 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-11-04 12:01 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 36 2012-11-04 12:01 ./usr/bin/tagBam
+-rwxr-xr-x root/root 36 2012-11-04 12:01 ./usr/bin/mapBed
+-rwxr-xr-x root/root 40 2012-11-04 12:01 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 12:01 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 43 2012-11-04 12:01 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 1194316 2012-11-04 12:01 ./usr/bin/bedtools
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 44 2012-11-04 12:01 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 40 2012-11-04 12:01 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 12:01 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 42 2012-11-04 12:01 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 41 2012-11-04 12:01 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 42 2012-11-04 12:01 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 37 2012-11-04 12:01 ./usr/bin/slopBed
+-rwxr-xr-x root/root 42 2012-11-04 12:01 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 39 2012-11-04 12:01 ./usr/bin/expandCols
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -924,7 +1059,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-86ea2b95-2c30-479d-b5b9-37e46d2328ad/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq
+Purging /var/lib/schroot/mount/sid-armel-sbuild-14d71a20-3ac0-4510-84f8-f149dea16908/build/buildd-bedtools_2.17.0-1-armel-z49NH1
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -932,19 +1067,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 75596
-Build-Time: 1701
+Build-Space: 78204
+Build-Time: 1718
Distribution: sid
-Install-Time: 160
-Job: bedtools_2.16.1-1
+Install-Time: 138
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 1981
-Source-Version: 2.16.1-1
-Space: 75596
+Package-Time: 1989
+Source-Version: 2.17.0-1
+Space: 78204
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1254
-Build needed 00:33:01, 75596k disc space
+Finished at 20121104-1201
+Build needed 00:33:09, 78204k disc space
Signature with key '4CB559DB' requested:
diff --git a/armhf.log b/armhf.log
index 54a1db3..ef3a45e 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,69 +1,60 @@
-From buildd at hasse.debian.org Fri Mar 16 14:04:16 2012
-Return-path: <buildd at hasse.debian.org>
+From buildd at hummel.debian.org Sun Nov 04 11:57:48 2012
+Return-path: <buildd at hummel.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at hasse.debian.org>)
- id 1S8XlP-0005R2-S1
- for logs at buildd.debian.org; Fri, 16 Mar 2012 14:04:16 +0000
-Received: from [217.140.96.68] (helo=hasse.debian.org)
+ (Exim 4.72) (envelope-from <buildd at hummel.debian.org>)
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+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:57:48 +0000
+Received: from hummel.ynic.york.ac.uk ([144.32.168.76] helo=hummel.debian.org)
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- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at hasse.debian.org>)
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-From: buildd on hasse <buildd at hasse.debian.org>
-To: logs at buildd.debian.org,buildd-porters at hasse.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on armhf (dist=sid)
+ CN=hummel.debian.org, EMAIL=hostmaster at hummel.debian.org (verified)
+ by merikanto.debian.org with esmtps
+ (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.72)
+ (envelope-from <buildd at hummel.debian.org>) id 1TUypm-00078u-IJ
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:57:46 +0000
+Received: from buildd by hummel.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at hummel.debian.org>)
+ id 1TUypj-0004cO-Jh; Sun, 04 Nov 2012 11:57:43 +0000
+From: buildd on hummel <buildd at hummel.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hummel.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1S8XlN-0000ff-L1 at hasse.debian.org>
-Date: Fri, 16 Mar 2012 14:04:13 +0000
+Message-Id: <E1TUypj-0004cO-Jh at hummel.debian.org>
+Date: Sun, 04 Nov 2012 11:57:43 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hasse.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hummel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (armhf) 16 Mar 2012 13:36 ║
+║ bedtools 2.17.0-1 (armhf) 04 Nov 2012 11:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: armhf
-Get:1 http://incoming.debian.org unstable InRelease [198 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [198 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6213 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [219 kB]
+Get:2 http://incoming.debian.org unstable InRelease [219 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6381 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.8 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [5650 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [35.6 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2223 B]
-Get:11 http://ftp.uk.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:12 http://ftp.uk.debian.org unstable/main Translation-en [3902 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main armhf Packages [5650 kB]
-Get:16 http://incoming.debian.org unstable/contrib armhf Packages [35.6 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [61.5 kB]
-Get:22 http://incoming.debian.org Packages [696 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.1 MB in 1min 19s (416 kB/s)
+Get:5 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.1 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [6006 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [35.8 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main armhf Packages [6006 kB]
+Get:13 http://incoming.debian.org unstable/contrib armhf Packages [35.8 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.8 MB in 1min 31s (281 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,12 +74,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 3s (285 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (615 kB/s)
Download complete and in download only mode
Check arch
@@ -102,34 +93,34 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5+b1)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-27)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1+b1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -140,10 +131,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -153,158 +144,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-0 upgraded, 32 newly installed, 0 to remove and 4 not upgraded.
-Need to get 16.4 MB of archives.
-After this operation, 42.0 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armhf 5.9-4+b1 [293 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armhf 1.0.0h-1 [962 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.10-1 [246 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 8.12-4+b1 [222 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.30.2-6 [1673 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.7.8.dfsg-7 [779 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.4-2 [134 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armhf 2.0.1-7.2+b1 [106 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armhf 4.8.30-11 [590 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.1 [203 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-6+b1 [1027 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.1-1 [1009 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.10-1 [52.4 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-5+b1 [132 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armhf 3.7.10-1 [371 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armhf 2.7.3~rc1-1 [1595 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armhf 2.7.3~rc1-1 [2635 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-5+b1 [1920 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:30 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-2 [27.4 kB]
-Get:31 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:32 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.6.dfsg-2 [206 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 1 not upgraded.
+Need to get 15.8 MB of archives.
+After this operation, 41.5 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armhf 5.9-10 [111 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.2-1 [33.7 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armhf 1.0.1c-4 [1018 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.31-1 [246 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armhf 3.7.14.1-1 [389 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-6 [786 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.33.12+really2.32.4-3 [1708 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.6-1 [120 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armhf 2.1.0-1 [109 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-9 [122 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.3-1 [1014 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-9 [130 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armhf 2.7.3-5 [1609 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armhf 2.7.3-5 [2650 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-9 [1828 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
+Get:32 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 16.4 MB in 4s (3526 kB/s)
-Selecting previously unselected package libncursesw5.
-(Reading database ... 12757 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_armhf.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_armhf.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_armhf.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_armhf.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_armhf.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_armhf.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_armhf.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_armhf.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2+b1_armhf.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_armhf.deb) ...
+Fetched 15.8 MB in 5s (2645 kB/s)
+Selecting previously unselected package libncursesw5:armhf.
+(Reading database ... 10832 files and directories currently installed.)
+Unpacking libncursesw5:armhf (from .../libncursesw5_5.9-10_armhf.deb) ...
+Selecting previously unselected package libpipeline1:armhf.
+Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.2-1_armhf.deb) ...
+Selecting previously unselected package libssl1.0.0:armhf.
+Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1c-4_armhf.deb) ...
+Selecting previously unselected package libasprintf0c2:armhf.
+Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ...
+Selecting previously unselected package libmagic1:armhf.
+Unpacking libmagic1:armhf (from .../libmagic1_5.11-2_armhf.deb) ...
+Selecting previously unselected package libpcre3:armhf.
+Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-1_armhf.deb) ...
+Selecting previously unselected package libsqlite3-0:armhf.
+Unpacking libsqlite3-0:armhf (from .../libsqlite3-0_3.7.14.1-1_armhf.deb) ...
+Selecting previously unselected package libxml2:armhf.
+Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-6_armhf.deb) ...
+Selecting previously unselected package libffi5:armhf.
+Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
+Selecting previously unselected package libglib2.0-0:armhf.
+Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.33.12+really2.32.4-3_armhf.deb) ...
+Selecting previously unselected package libcroco3:armhf.
+Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-1_armhf.deb) ...
+Selecting previously unselected package libexpat1:armhf.
+Unpacking libexpat1:armhf (from .../libexpat1_2.1.0-1_armhf.deb) ...
+Selecting previously unselected package libunistring0:armhf.
+Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
+Selecting previously unselected package libgettextpo0:armhf.
+Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6+b1_armhf.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_armhf.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_armhf.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_armhf.deb) ...
+Unpacking file (from .../archives/file_5.11-2_armhf.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_armhf.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_armhf.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_armhf.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_armhf.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_armhf.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_armhf.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5+b1_armhf.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_armhf.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armhf.deb) ...
-Setting up libncursesw5 (5.9-4+b1) ...
-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+b1) ...
-Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:armhf.
+Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armhf.deb) ...
+Setting up libncursesw5:armhf (5.9-10) ...
+Setting up libpipeline1:armhf (1.2.2-1) ...
+Setting up libssl1.0.0:armhf (1.0.1c-4) ...
+Setting up libasprintf0c2:armhf (0.18.1.1-9) ...
+Setting up libmagic1:armhf (5.11-2) ...
+Setting up libpcre3:armhf (1:8.31-1) ...
+Setting up libsqlite3-0:armhf (3.7.14.1-1) ...
+Setting up libxml2:armhf (2.8.0+dfsg1-6) ...
+Setting up libffi5:armhf (3.0.10-3+b1) ...
+Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-7) ...
-Setting up libcroco3 (0.6.4-2) ...
-Setting up libexpat1 (2.0.1-7.2+b1) ...
-Setting up libunistring0 (0.9.3-5+b1) ...
-Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:armhf (0.6.6-1) ...
+Setting up libexpat1:armhf (2.1.0-1) ...
+Setting up libunistring0:armhf (0.9.3-5+b1) ...
+Setting up libgettextpo0:armhf (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5+b1) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-5+b1) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:armhf (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-2-mx5 armhf (armv7l)
-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_3.2.9-1
-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+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2012.01.08 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-4.4-base_4.4.6-15 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-3 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libalgorithm-diff-perl_1.19.02-2 libalgorithm-merge-perl_0.08-2 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+b1 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-4 libmpc2_0.9-4+b1 libmpfr4_3.1.0-4 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 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+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 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+b1 libunistring0_0.9.3-5+b1 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_3.2.9-1 login_1:4.1.5-1 lsb-base_3.2+Debian31 make_3.81-8.1+b1 man-db_2.6.1-1 manpages_3.35-0.1 manpages-dev_3.35-0.1 mawk_1.3.3-16+b1 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+b1 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 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 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+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Kernel: Linux 3.2.0-3-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -315,12 +311,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -331,18 +327,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture armhf
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -358,11 +354,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -370,30 +366,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -404,7 +402,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -479,7 +477,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -488,7 +486,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -538,10 +536,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -564,6 +565,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -607,7 +609,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -631,7 +633,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -645,6 +647,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -718,16 +721,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0'
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
@@ -743,78 +768,85 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org> >../bedtools_2.16.1-1_armhf.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org> >../bedtools_2.17.0-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1404
+Build finished at 20121104-1157
-bedtools_2.16.1-1_armhf.changes:
+bedtools_2.17.0-1_armhf.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: armhf
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org>
+Maintainer: armhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 09871415f8afe7fef890051540cec22ff76c99a6 383636 bedtools_2.16.1-1_armhf.deb
+ 16d01a70af9713f8071176b2c71a43d558e355ca 400610 bedtools_2.17.0-1_armhf.deb
Checksums-Sha256:
- f20bb01e537268a79e5789862157e61ed7f59845a6657db886f750778f4fb553 383636 bedtools_2.16.1-1_armhf.deb
+ e45b2cd9994a2c1b02e13a5f91a656fdfbaa948b1dbb7dabb19c2471090f39e5 400610 bedtools_2.17.0-1_armhf.deb
Files:
- 66425f372ea8459df6508fec03eaa213 383636 science optional bedtools_2.16.1-1_armhf.deb
+ 261f24cfbd23e451266850895c273031 400610 science optional bedtools_2.17.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_armhf.deb
+bedtools_2.17.0-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 383636 bytes: control archive= 1972 bytes.
- 864 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 400610 bytes: control archive=4117 bytes.
+ 32 bytes, 1 lines conffiles
+ 837 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 958
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1116
+ Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -828,58 +860,168 @@ bedtools_2.16.1-1_armhf.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/subtractBed
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/coverageBed
--rwxr-xr-x root/root 919800 2012-03-16 14:03 ./usr/bin/bedtools
--rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/linksBed
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/nucBed
--rwxr-xr-x root/root 36 2012-03-16 14:03 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/mergeBed
--rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/tagBam
--rwxr-xr-x root/root 29 2012-03-16 14:03 ./usr/bin/sortBed
--rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/getOverlap
--rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/mapBed
--rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/bamToBed
--rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/expandCols
--rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/intersectBed
--rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/pairToBed
--rwxr-xr-x root/root 36 2012-03-16 14:03 ./usr/bin/windowMaker
--rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/closestBed
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/windowBed
--rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/clusterBed
--rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 29 2012-03-16 14:03 ./usr/bin/slopBed
--rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/flankBed
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/annotateBed
--rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/randomBed
--rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/bedToBam
--rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/pairToPair
--rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/complementBed
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 13:39 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/bin/
+-rwxr-xr-x root/root 38 2012-11-04 11:56 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 42 2012-11-04 11:56 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 42 2012-11-04 11:56 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 42 2012-11-04 11:56 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 40 2012-11-04 11:56 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 11:56 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 40 2012-11-04 11:56 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 44 2012-11-04 11:56 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 36 2012-11-04 11:56 ./usr/bin/tagBam
+-rwxr-xr-x root/root 38 2012-11-04 11:56 ./usr/bin/linksBed
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 40 2012-11-04 11:56 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 39 2012-11-04 11:56 ./usr/bin/expandCols
+-rwxr-xr-x root/root 38 2012-11-04 11:56 ./usr/bin/flankBed
+-rwxr-xr-x root/root 37 2012-11-04 11:56 ./usr/bin/slopBed
+-rwxr-xr-x root/root 36 2012-11-04 11:56 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 40 2012-11-04 11:56 ./usr/bin/closestBed
+-rwxr-xr-x root/root 936192 2012-11-04 11:57 ./usr/bin/bedtools
+-rwxr-xr-x root/root 42 2012-11-04 11:56 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:56 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 43 2012-11-04 11:56 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 39 2012-11-04 11:56 ./usr/bin/randomBed
+-rwxr-xr-x root/root 36 2012-11-04 11:56 ./usr/bin/nucBed
+-rwxr-xr-x root/root 43 2012-11-04 11:56 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 43 2012-11-04 11:56 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 39 2012-11-04 11:56 ./usr/bin/windowBed
+-rwxr-xr-x root/root 43 2012-11-04 11:56 ./usr/bin/complementBed
+-rwxr-xr-x root/root 37 2012-11-04 11:56 ./usr/bin/sortBed
+-rwxr-xr-x root/root 36 2012-11-04 11:56 ./usr/bin/mapBed
+-rwxr-xr-x root/root 42 2012-11-04 11:56 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 44 2012-11-04 11:56 ./usr/bin/bed12ToBed6
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:57 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -893,7 +1035,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-55323db0-9268-44ad-b050-6eb0a35707d6/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-749f582d-3064-46da-beab-12826efb95ab/build/buildd-bedtools_2.17.0-1-armhf-sVT5Vc
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -901,19 +1043,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 75200
-Build-Time: 1464
+Build-Space: 78308
+Build-Time: 1510
Distribution: sid
-Install-Time: 92
-Job: bedtools_2.16.1-1
+Install-Time: 147
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 1668
-Source-Version: 2.16.1-1
-Space: 75200
+Package-Time: 1781
+Source-Version: 2.17.0-1
+Space: 78308
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1404
-Build needed 00:27:48, 75200k disc space
-Signature with key '0B213A80' requested:
+Finished at 20121104-1157
+Build needed 00:29:41, 78308k disc space
+Signature with key '630B2C7A' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 71ab708..127441d 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,60 +1,64 @@
-From buildd at mozart.debian.net Fri Mar 16 12:33:55 2012
-Return-path: <buildd at mozart.debian.net>
-Received: from callisto.debian.net ([80.87.129.151])
+From buildd at ironforge.sceen.net Sun Nov 04 13:55:21 2012
+Return-path: <buildd at ironforge.sceen.net>
+Received: from ironforge.sceen.net ([46.105.42.111])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
- id 1S8WLy-0005l6-4d
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:33:55 +0000
-Received: from mozart.debian.net ([10.1.0.1])
- by callisto.debian.net with esmtp (Exim 4.72)
- (envelope-from <buildd at mozart.debian.net>)
- id 1S8WLt-00086O-Nq; Fri, 16 Mar 2012 12:33:49 +0000
-Received: from buildd by mozart.debian.net with local (Exim 4.76)
- (envelope-from <buildd at mozart.debian.net>)
- id 1S8WM1-0002kj-KW; Fri, 16 Mar 2012 12:33:57 +0000
-From: Build Daemon <buildd at mozart.debian.net>
-To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
- logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on hurd-i386 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1S8WM1-0002kj-KW at mozart.debian.net>
-Date: Fri, 16 Mar 2012 12:33:57 +0000
+ (Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
+ id 1TV0fY-0005vN-S6
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 13:55:21 +0000
+Received: from buildd by ironforge.sceen.net with local (Exim 4.77)
+ (envelope-from <buildd at ironforge.sceen.net>)
+ id 1TV0ff-0004BY-6S; Sun, 04 Nov 2012 14:55:27 +0100
+Content-Transfer-Encoding: binary
+MIME-Version: 1.0
+X-Mailer: MIME::Lite 3.027 (F2.82; B3.13; Q3.13)
+Date: Sun, 4 Nov 2012 14:55:27 +0100
+From: Build Daemon <buildd at ironforge.sceen.net>
+To: samuel.thibault at ens-lyon.org,mbanck at gmx.net,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on hurd-i386 (dist=sid)
+Message-Id: <E1TV0ff-0004BY-6S at ironforge.sceen.net>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mozart.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (hurd-i386) 16 mars 2012 12:15 ║
+║ bedtools 2.17.0-1 (hurd-i386) 04 Nov 2012 14:51 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: hurd-i386
+Ign file: ./ InRelease
+Ign file: ./ Release.gpg
+Ign file: ./ Release
+Ign file: ./ Translation-en
Hit http://ftp.fr.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
-Ign http://ftp.debian-ports.org unreleased InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.fr.debian.org sid/main TranslationIndex
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:2 http://incoming.debian.org Release [1616 B]
-Hit http://ftp.fr.debian.org sid/contrib Translation-en
-Hit http://ftp.fr.debian.org sid/main Translation-en
-Get:3 http://incoming.debian.org Sources [58.9 kB]
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Get:4 http://incoming.debian.org Packages [687 kB]
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Hit http://ftp.fr.debian.org sid/contrib Translation-en/DiffIndex
+Hit http://ftp.fr.debian.org sid/main Translation-en/DiffIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
+Hit http://incoming.debian.org sid/main Translation-en/DiffIndex
+Get:2 http://incoming.debian.org Release [1141 B]
+Ign http://incoming.debian.org sid/main 2012-11-04-0210.01.pdiff
+Ign http://incoming.debian.org sid/main hurd-i386 2012-11-04-0210.01.pdiff
+Get:3 http://incoming.debian.org Sources [19.3 kB]
+Get:4 http://incoming.debian.org Packages [180 kB]
+Hit http://incoming.debian.org sid/main
+Hit http://incoming.debian.org sid/main hurd-i386
Ign http://incoming.debian.org Translation-en
-Fetched 748 kB in 1min 2s (12.0 kB/s)
+Fetched 201 kB in 9s (22.0 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,12 +78,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 4s (198 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 4s (244 kB/s)
Download complete and in download only mode
Check arch
@@ -92,142 +96,202 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1+hurd.1)
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3+hurd.1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42.1-2)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.3.12-9)
-hostname: already installed (3.06)
-hurd: already installed (20111206-1)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-sysvinit-utils: already installed (2.88dsf-13.13)
-sysvinit: already installed (2.88dsf-13.13)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc0.3-dev: already installed (2.13-25)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
-hurd-dev: already installed (20111206-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3+b1)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6+b1)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-4+b1)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11+b1)
+hurd: already installed (20120710-3)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4+b1)
+bsdutils: already installed (1:2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc0.3-dev: already installed (2.13-35)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2+b1)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+hurd-dev: already installed (20120710-3)
cdbs: missing
-debhelper: already installed (9.20120115 >= 8 is satisfied)
+debhelper: missing
+Using default version 9.20120909
quilt: missing
python: missing
-zlib1g-dev: already installed (1:1.2.6.dfsg-1)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs quilt python
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat libdb4.8 libsqlite3-0 mime-support python-minimal python2.7
- python2.7-minimal
+ diffstat file gettext gettext-base html2text intltool-debian libasprintf0c2
+ libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0 libmagic1
+ libsqlite3-0 libunistring0 libxml2 mime-support po-debconf python-minimal
+ python2.7 python2.7-minimal
Suggested packages:
- devscripts python-doc python-tk python2.7-doc binfmt-support procmail
- graphviz default-mta mail-transport-agent
+ devscripts dh-make gettext-doc libmail-box-perl python-doc python-tk
+ python2.7-doc binfmt-support procmail graphviz default-mta
+ mail-transport-agent
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs diffstat libdb4.8 libsqlite3-0 mime-support python python-minimal
- python2.7 python2.7-minimal quilt
-0 upgraded, 10 newly installed, 0 to remove and 89 not upgraded.
-Need to get 0 B/6107 kB of archives.
-After this operation, 18.6 MB of additional disk space will be used.
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libsqlite3-0 libunistring0 libxml2 mime-support po-debconf python
+ python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 36 not upgraded.
+Need to get 0 B/12.6 MB of archives.
+After this operation, 37.2 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- libdb4.8 libsqlite3-0 mime-support python2.7-minimal python2.7
- python-minimal python cdbs diffstat quilt
+ libasprintf0c2 libmagic1 libsqlite3-0 libxml2 libffi5 libglib2.0-0 libcroco3
+ libexpat1 libunistring0 libgettextpo0 file gettext-base mime-support
+ python2.7-minimal python2.7 python-minimal python cdbs html2text gettext
+ intltool-debian po-debconf debhelper diffstat quilt zlib1g-dev
Authentication warning overridden.
-Selecting previously unselected package libdb4.8.
-(Reading database ... 15865 files and directories currently installed.)
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_hurd-i386.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_hurd-i386.deb) ...
+Selecting previously unselected package libasprintf0c2:hurd-i386.
+(Reading database ... 15297 files and directories currently installed.)
+Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package libmagic1:hurd-i386.
+Unpacking libmagic1:hurd-i386 (from .../libmagic1_5.11-2_hurd-i386.deb) ...
+Selecting previously unselected package libsqlite3-0:hurd-i386.
+Unpacking libsqlite3-0:hurd-i386 (from .../libsqlite3-0_3.7.14.1-1_hurd-i386.deb) ...
+Selecting previously unselected package libxml2:hurd-i386.
+Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-6_hurd-i386.deb) ...
+Selecting previously unselected package libffi5:hurd-i386.
+Unpacking libffi5:hurd-i386 (from .../libffi5_3.0.10-3+b1_hurd-i386.deb) ...
+Selecting previously unselected package libglib2.0-0:hurd-i386.
+Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_hurd-i386.deb) ...
+Selecting previously unselected package libcroco3:hurd-i386.
+Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.6-1_hurd-i386.deb) ...
+Selecting previously unselected package libexpat1:hurd-i386.
+Unpacking libexpat1:hurd-i386 (from .../libexpat1_2.1.0-1+b1_hurd-i386.deb) ...
+Selecting previously unselected package libunistring0:hurd-i386.
+Unpacking libunistring0:hurd-i386 (from .../libunistring0_0.9.3-5+b1_hurd-i386.deb) ...
+Selecting previously unselected package libgettextpo0:hurd-i386.
+Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_5.11-2_hurd-i386.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_hurd-i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_hurd-i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_hurd-i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-11_hurd-i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_hurd-i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b2_hurd-i386.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_hurd-i386.deb) ...
+Selecting previously unselected package intltool-debian.
+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_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_hurd-i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_hurd-i386.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:hurd-i386.
+Unpacking zlib1g-dev:hurd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_hurd-i386.deb) ...
Processing triggers for man-db ...
-Setting up libdb4.8 (4.8.30-11) ...
-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 (2.7.2-11) ...
-Setting up python2.7 (2.7.2-11) ...
-Setting up python-minimal (2.7.2-10) ...
-Setting up python (2.7.2-10) ...
-Setting up cdbs (0.4.109) ...
-Setting up diffstat (1.55-2) ...
+Setting up libasprintf0c2:hurd-i386 (0.18.1.1-9) ...
+Setting up libmagic1:hurd-i386 (5.11-2) ...
+Setting up libsqlite3-0:hurd-i386 (3.7.14.1-1) ...
+Setting up libxml2:hurd-i386 (2.8.0+dfsg1-6) ...
+Setting up libffi5:hurd-i386 (3.0.10-3+b1) ...
+Setting up libglib2.0-0:hurd-i386 (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:hurd-i386 (0.6.6-1) ...
+Setting up libexpat1:hurd-i386 (2.1.0-1+b1) ...
+Setting up libunistring0:hurd-i386 (0.9.3-5+b1) ...
+Setting up libgettextpo0:hurd-i386 (0.18.1.1-9) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
+Setting up html2text (1.3.2a-15+b2) ...
+Setting up gettext (0.18.1.1-9) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:hurd-i386 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.22-5+hurd.1 dpkg-dev_1.16.1.1 g++-4.5_4.5.3-9 g++-4.6_4.6.2-16+hurd.1 gcc-4.4_4.4.6-14 gcc-4.5_4.5.3-9 gcc-4.6_4.6.2-16+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20111206-1 libc0.3-dev_2.13-25 libstdc++6_4.6.2-16+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.2-16+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.22-5+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.4_4.4.6-14 cpp-4.5_4.5.3-9 cpp-4.6_4.6.2-16+hurd.1 cron_3.0pl1-120 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120115 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2012.01.08 debianutils_4.0.4 deborphan_1.7.28.5 dialog_1.1-20111020-1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.1-1+hurd.1 file_5.10-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3.1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.2-16+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.2-4 gcc-4.4_4.4.6-14 gcc-4.4-base_4.4.6-14 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-16+hurd.1 gcc-4.6-base_4.6.2-16+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.6_4.6.2-16+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-14 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20111206-1 hurd-dev_20111206-1 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libapt-pkg-dev_0.8.15.9 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libboost-iostreams1.46.1_1.46.1-8 libboost-iostreams1.48.0_1.48.0-3 libbz2-1.0_1.0.6-1 libc-bin_2.13-25 libc-dev-bin_2.13-25 libc0.3_2.13-25 libc0.3-dev_2.13-25 libc0.3-xen_2.13-25 libclass-isa-perl_0.36-2 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libcwidget3_0.5.16-3.1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.1 libelfg0_0.8.13-3 libept-dev_1.0.5 libept1_1.0.5 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libfontconfig1_2.8.0-3.1 libfreetype6_2.4.8-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-16+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.2-16+hurd.1 libglib2.0-0_2.30.2-6 libglib2.0-data_2.28.8-1 libgmp10_2:5.0.4+dfsg-1 libgnutls26_2.12.17-2 libgomp1_4.6.2-16+hurd.1 libgpg-error0_1.10-3 libldap-2.4-2_2.4.28-1.1 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libobjc2_4.5.3-9 libp11-kit0_0.12-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-7 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.47-1 libpopt0_1.16-3 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.2-16+hurd.1 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-4 libsasl2-modules_2.1.25.dfsg1-4 libsigc++-2.0-0c2a_2.2.9-1.1 libsigsegv2_2.9-4 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-16+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.2-16+hurd.1 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.13-1 libtasn1-3_2.11-1 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.20.1-4 libwibble-dev_0.1.26-1 libxapian-dev_1.2.7-1 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-7 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mime-support_3.52-1 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.16-1+hurd.1 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011n-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-1 zlib1g-dev_1:1.2.6.dfsg-1
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 gnumach-dev_2:1.3.99.dfsg.git20120923-1 hurd-dev_20120710-3 libc0.3-dev_2.13-35 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: adduser_3.113+nmu3 apt_0.9.7.4 apt-utils_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpio_2.11-8 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3+b1 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6+b1 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4+b1 g++_4:4.7.1-1 g++-4.7_4.7.2-4 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.2-1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-12 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnumach-dev_2:1.3.99.dfsg.git20120923-1 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11+b1 html2text_1.3.2a-15+b2 hurd_20120710-3 hurd-dev_20120710-3 initscripts_2.88dsf-22 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.5 libapt-pkg4.12_0.9.7.5 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc0.3_2.13-35 libc0.3-dev_2.13-35 libc0.3-i686_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.9 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgcrypt11_1.5.0-3+b1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-1 libgomp1_4.7.2-4 libgpg-error0_1.10-3.1 libldap-2.4-2_2.4.28-1.3+b2 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libparted0debian1_2.3-11 libpciaccess0_0.13.1-2+b2 libpcre3_1:8.31-1 libpipeline1_1.2.1-1+b1 libpng12-0_1.2.49-3 libpopt0_1.16-7 libprocps0_1:3.3.3-2 libpthread-stubs0_0.3-3 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsasl2-2_2.1.25.dfsg1-5 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1.2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.2 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxapian22_1.2.8-1 libxau6_1:1.0.7-1+b1 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1+b1 libxml2_2.8.0+dfsg1-6 lsb-base_4.1+Debian7 make_3.81-8.2+b1 man-db_2.6.2-1 mawk_1.3.3-17+b1 mime-support_3.52-2 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20120710-1 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 procps_1:3.3.3-2 psmisc_22.19-1 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4+b1 tzdata_2012e-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xkb-data_2.5.1-2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -238,12 +302,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -254,18 +318,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -281,11 +345,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -293,30 +357,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -327,7 +393,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -402,16 +468,16 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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]
+bamToBed.cpp:85:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
+ * compiling bamToBed.cpp
- Building in src/bamToFastq
* compiling bamToFastqMain.cpp
bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
@@ -422,9 +488,9 @@ bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunu
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]
+ * compiling bedpeToBam.cpp
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- Building in src/bed12ToBed6
@@ -433,9 +499,9 @@ bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused
* 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 clusterMain.cpp
* compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
@@ -455,16 +521,19 @@ clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wu
* 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]
+ * compiling getOverlap.cpp
- Building in src/groupBy
- * compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+ * compiling groupBy.cpp
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -478,15 +547,16 @@ mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but
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 mergeMain.cpp
* 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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -499,18 +569,18 @@ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used
* 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 pairToBedMain.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
- Building in src/pairToPair
- * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling pairToPairMain.cpp
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
@@ -528,21 +598,21 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
* 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling subtractMain.cpp
* 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 tagBamMain.cpp
* compiling tagBam.cpp
- Building in src/unionBedGraphs
- * compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
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 unionBedGraphsMain.cpp
* compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
@@ -554,7 +624,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -568,6 +638,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -641,16 +712,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0'
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
@@ -666,8 +759,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -677,66 +773,70 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.16.1-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../bedtools_2.17.0-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1232
+Build finished at 20121104-1455
-bedtools_2.16.1-1_hurd-i386.changes:
+bedtools_2.17.0-1_hurd-i386.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- ebc62c6fbc856685c98460882a23493fcf1d8267 443564 bedtools_2.16.1-1_hurd-i386.deb
+ 34885c33aed021ef2549de98f66d6267d8a581ef 448554 bedtools_2.17.0-1_hurd-i386.deb
Checksums-Sha256:
- e1f4ed7099dc003fe3dcf6f58de97f708e677657f9f213b467a79e4f37f56e5a 443564 bedtools_2.16.1-1_hurd-i386.deb
+ 311dabecb708560a550150907f580321f866b6e29a467f219b9642e40c89f466 448554 bedtools_2.17.0-1_hurd-i386.deb
Files:
- 34f11720cbc1244c01aac14d545c7152 443564 science optional bedtools_2.16.1-1_hurd-i386.deb
+ a39a5b4956d88fd0c5693c25d01f03f5 448554 science optional bedtools_2.17.0-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_hurd-i386.deb
+bedtools_2.17.0-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 443564 bytes: control archive= 1984 bytes.
- 869 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 448554 bytes: control archive= 4110 bytes.
+ 32 bytes, 1 lines conffiles
+ 837 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1430
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1528
+ Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -750,58 +850,168 @@ bedtools_2.16.1-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:31 ./
-drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:32 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:19 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2012-03-16 12:32 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 12:30 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/bedToBam
--rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 1403068 2012-03-16 12:32 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/coverageBed
--rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/flankBed
--rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/intersectBed
--rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/mapBed
--rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/pairToBed
--rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/pairToPair
--rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 29 2012-03-16 12:30 ./usr/bin/slopBed
--rwxr-xr-x root/root 29 2012-03-16 12:30 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/tagBam
--rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-03-16 12:30 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 18:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 06:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 18:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 09:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 14:51 ./usr/share/bedtools/genomes/
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+-rw-r--r-- root/root 10172 2012-11-03 18:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
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+-rw-r--r-- root/root 167 2012-11-03 18:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
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+-rw-r--r-- root/root 825 2012-11-03 18:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
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+-rw-r--r-- root/root 2753 2012-11-03 18:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 147 2012-11-03 18:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 186 2012-11-03 18:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 227 2012-11-03 18:11 ./usr/share/bedtools/test/map/values3.bed
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+-rw-r--r-- root/root 147 2012-11-03 18:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 57 2012-11-03 18:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 18:11 ./usr/share/bedtools/test/merge/test-merge.sh
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+-rw-r--r-- root/root 96 2012-11-03 18:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 18:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 18:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 18:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 167 2012-11-03 18:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
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+-rw-r--r-- root/root 3603 2012-11-03 18:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 18:11 ./usr/share/bedtools/test/slop/tiny.genome
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+-rw-r--r-- root/root 36 2012-11-03 18:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 18:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 2532 2012-11-03 18:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 1243 2012-11-03 18:11 ./usr/share/bedtools/test/test.sh
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+-rwxr-xr-x root/root 43 2012-11-04 14:54 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 44 2012-11-04 14:54 ./usr/bin/bed12ToBed6
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+-rwxr-xr-x root/root 41 2012-11-04 14:54 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-11-04 14:54 ./usr/bin/bedToIgv
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+-rwxr-xr-x root/root 40 2012-11-04 14:54 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 14:54 ./usr/bin/complementBed
+-rwxr-xr-x root/root 41 2012-11-04 14:54 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 39 2012-11-04 14:54 ./usr/bin/expandCols
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+-rwxr-xr-x root/root 42 2012-11-04 14:54 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 40 2012-11-04 14:54 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 42 2012-11-04 14:54 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 38 2012-11-04 14:54 ./usr/bin/linksBed
+-rwxr-xr-x root/root 36 2012-11-04 14:54 ./usr/bin/mapBed
+-rwxr-xr-x root/root 42 2012-11-04 14:54 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 14:54 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 14:54 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 43 2012-11-04 14:54 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 36 2012-11-04 14:54 ./usr/bin/nucBed
+-rwxr-xr-x root/root 42 2012-11-04 14:54 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 43 2012-11-04 14:54 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 39 2012-11-04 14:54 ./usr/bin/randomBed
+-rwxr-xr-x root/root 40 2012-11-04 14:54 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 37 2012-11-04 14:54 ./usr/bin/slopBed
+-rwxr-xr-x root/root 37 2012-11-04 14:54 ./usr/bin/sortBed
+-rwxr-xr-x root/root 41 2012-11-04 14:54 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-11-04 14:54 ./usr/bin/tagBam
+-rwxr-xr-x root/root 42 2012-11-04 14:54 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 39 2012-11-04 14:54 ./usr/bin/windowBed
+-rwxr-xr-x root/root 44 2012-11-04 14:54 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 14:54 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 09:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -815,44 +1025,72 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.17.0-1-hurd-i386-z_Ffqp
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
- libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
+ adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
+ libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
+ man-db
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* diffstat* libdb4.8* libsqlite3-0* mime-support* python*
- python-minimal* python2.7* python2.7-minimal* quilt*
-0 upgraded, 0 newly installed, 10 to remove and 89 not upgraded.
-After this operation, 18.6 MB disk space will be freed.
-(Reading database ... 16834 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libasprintf0c2* libcroco3* libexpat1* libffi5*
+ libgettextpo0* libglib2.0-0* libmagic1* libsqlite3-0* libunistring0*
+ libxml2* mime-support* po-debconf* python* python-minimal* python2.7*
+ python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 26 to remove and 36 not upgraded.
+After this operation, 37.2 MB disk space will be freed.
+(Reading database ... 17249 files and directories currently installed.)
Removing cdbs ...
+Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:hurd-i386 ...
+Removing libcroco3:hurd-i386 ...
+Purging configuration files for libcroco3:hurd-i386 ...
Removing python ...
Purging configuration files for python ...
Removing python2.7 ...
Purging configuration files for python2.7 ...
-Removing libdb4.8 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
+Removing libexpat1:hurd-i386 ...
+Purging configuration files for libexpat1:hurd-i386 ...
+Removing libglib2.0-0:hurd-i386 ...
+Purging configuration files for libglib2.0-0:hurd-i386 ...
+Removing libffi5:hurd-i386 ...
+Purging configuration files for libffi5:hurd-i386 ...
+Removing libgettextpo0:hurd-i386 ...
+Removing libmagic1:hurd-i386 ...
+Purging configuration files for libmagic1:hurd-i386 ...
+Removing libsqlite3-0:hurd-i386 ...
+Purging configuration files for libsqlite3-0:hurd-i386 ...
+Removing libunistring0:hurd-i386 ...
+Purging configuration files for libunistring0:hurd-i386 ...
+Removing libxml2:hurd-i386 ...
+Purging configuration files for libxml2:hurd-i386 ...
Removing mime-support ...
Purging configuration files for mime-support ...
Removing python-minimal ...
Removing python2.7-minimal ...
Purging configuration files for python2.7-minimal ...
+Removing zlib1g-dev:hurd-i386 ...
Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -860,18 +1098,17 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 71620
-Build-Time: 788
+Build-Space: 74768
+Build-Time: 215
Distribution: sid
-Install-Time: 114
-Job: bedtools_2.16.1-1
+Install-Time: 20
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 1049
-Source-Version: 2.16.1-1
-Space: 71620
+Package-Time: 255
+Source-Version: 2.17.0-1
+Space: 74768
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1232
-Build needed 00:17:29, 71620k disc space
-
+Finished at 20121104-1455
+Build needed 00:04:15, 74768k disc space
diff --git a/i386.log b/i386.log
index 5af347d..4e5b226 100644
--- a/i386.log
+++ b/i386.log
@@ -1,70 +1,64 @@
-From buildd at biber.debian.org Fri Mar 16 12:53:00 2012
-Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at murphy.debian.org Sun Nov 04 11:37:39 2012
+Return-path: <buildd at murphy.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
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- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:52:59 +0000
-Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
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+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:37:39 +0000
+Received: from murphy.debian.org ([70.103.162.31])
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- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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- (envelope-from <buildd at biber.debian.org>)
- id 1S8WeP-0005SP-R3; Fri, 16 Mar 2012 12:52:57 +0000
-Message-Id: <E1S8WeP-0005SP-R3 at biber.debian.org>
+ CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
+ id 1TUyWH-0005No-Qa
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:37:38 +0000
+Received: from buildd by murphy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at murphy.debian.org>)
+ id 1TUyWF-0006f1-L0; Sun, 04 Nov 2012 11:37:35 +0000
+Message-Id: <E1TUyWF-0006f1-L0 at murphy.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 12:52:57 +0000
-From: buildd on biber <buildd at biber.debian.org>
-To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on i386 (dist=sid)
-Key-Id: 6EBCB100
+Date: Sun, 4 Nov 2012 11:37:35 +0000
+From: buildd on murphy <buildd at murphy.debian.org>
+To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on i386 (dist=sid)
+Key-Id: 2B54027C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (i386) 16 Mar 2012 12:47 ║
+║ bedtools 2.17.0-1 (i386) 04 Nov 2012 11:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [198 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [6213 kB]
-Get:3 http://ftp.gr.debian.org unstable/contrib Sources [54.4 kB]
-Get:4 http://ftp.gr.debian.org unstable/non-free Sources [99.8 kB]
-Get:5 http://ftp.gr.debian.org unstable/main i386 Packages [5912 kB]
-Get:6 http://incoming.debian.org unstable InRelease [198 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [45.6 kB]
-Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2223 B]
-Get:9 http://ftp.gr.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:10 http://ftp.gr.debian.org unstable/main Translation-en [3902 kB]
+Hit http://ftp.us.debian.org sid InRelease
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:11 http://incoming.debian.org Release.gpg [836 B]
-Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main i386 Packages [5912 kB]
-Get:16 http://incoming.debian.org unstable/contrib i386 Packages [45.6 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [60.2 kB]
-Get:22 http://incoming.debian.org Packages [696 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.7 MB in 21s (1542 kB/s)
+Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
+Get:1 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:2 http://incoming.debian.org sid/main i386 Packages/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
+Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
+Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Ign http://incoming.debian.org sid/main 2012-11-04-0210.01.pdiff
+Ign http://incoming.debian.org sid/main i386 2012-11-04-0210.01.pdiff
+Get:4 http://incoming.debian.org Release [1141 B]
+Hit http://incoming.debian.org sid/main
+Hit http://incoming.debian.org sid/main i386
+Get:5 http://incoming.debian.org Sources [16.2 kB]
+Get:6 http://incoming.debian.org Packages [140 kB]
+Fetched 174 kB in 3s (43.6 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,12 +78,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 3s (312 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 3s (330 kB/s)
Download complete and in download only mode
Check arch
@@ -103,58 +97,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.7)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-2)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.5-1)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-4)
-mount: already installed (2.20.1-4)
-util-linux: already installed (2.20.1-4)
-libc6-dev: already installed (2.13-27)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -165,10 +159,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -178,158 +172,129 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-0 upgraded, 32 newly installed, 0 to remove and 11 not upgraded.
-Need to get 19.3 MB of archives.
-After this operation, 52.7 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libncursesw5 i386 5.9-4 [330 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.1-1 [38.6 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main libssl1.0.0 i386 1.0.0h-1 [2862 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.10-1 [249 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.30.2-6 [1823 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-7 [885 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.4-2 [151 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libexpat1 i386 2.0.1-7.2 [137 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libdb4.8 i386 4.8.30-11 [729 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.1 [205 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.1-1 [1052 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.10-1 [52.4 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-5 [133 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main libsqlite3-0 i386 3.7.10-1 [442 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main python2.7-minimal i386 2.7.3~rc1-1 [1719 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main python2.7 i386 2.7.3~rc1-1 [2693 kB]
-Get:22 http://ftp.gr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:23 http://ftp.gr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:24 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:25 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:26 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-5 [2025 kB]
-Get:27 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:28 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:29 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:30 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-2 [29.3 kB]
-Get:31 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:32 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.6.dfsg-2 [210 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 19.3 MB in 1s (10.6 MB/s)
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10798 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_i386.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_i386.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_i386.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_i386.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_i386.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_i386.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_i386.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_i386.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_i386.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_i386.deb) ...
+0 upgraded, 33 newly installed, 0 to remove and 22 not upgraded.
+Need to get 0 B/18.7 MB of archives.
+After this operation, 51.3 MB of additional disk space will be used.
+Selecting previously unselected package libncursesw5:i386.
+(Reading database ... 11010 files and directories currently installed.)
+Unpacking libncursesw5:i386 (from .../libncursesw5_5.9-10_i386.deb) ...
+Selecting previously unselected package libpipeline1:i386.
+Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.2-1_i386.deb) ...
+Selecting previously unselected package libssl1.0.0:i386.
+Unpacking libssl1.0.0:i386 (from .../libssl1.0.0_1.0.1c-4_i386.deb) ...
+Selecting previously unselected package libasprintf0c2:i386.
+Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-9_i386.deb) ...
+Selecting previously unselected package libmagic1:i386.
+Unpacking libmagic1:i386 (from .../libmagic1_5.11-2_i386.deb) ...
+Selecting previously unselected package libpcre3:i386.
+Unpacking libpcre3:i386 (from .../libpcre3_1%3a8.31-1_i386.deb) ...
+Selecting previously unselected package libsqlite3-0:i386.
+Unpacking libsqlite3-0:i386 (from .../libsqlite3-0_3.7.14.1-1_i386.deb) ...
+Selecting previously unselected package libxml2:i386.
+Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-6_i386.deb) ...
+Selecting previously unselected package libffi5:i386.
+Unpacking libffi5:i386 (from .../libffi5_3.0.10-3_i386.deb) ...
+Selecting previously unselected package libglib2.0-0:i386.
+Unpacking libglib2.0-0:i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_i386.deb) ...
+Selecting previously unselected package libcroco3:i386.
+Unpacking libcroco3:i386 (from .../libcroco3_0.6.6-1_i386.deb) ...
+Selecting previously unselected package libexpat1:i386.
+Unpacking libexpat1:i386 (from .../libexpat1_2.1.0-1_i386.deb) ...
+Selecting previously unselected package libunistring0:i386.
+Unpacking libunistring0:i386 (from .../libunistring0_0.9.3-5_i386.deb) ...
+Selecting previously unselected package libgettextpo0:i386.
+Unpacking libgettextpo0:i386 (from .../libgettextpo0_0.18.1.1-9_i386.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_i386.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_i386.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_i386.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_i386.deb) ...
+Unpacking file (from .../archives/file_5.11-2_i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_i386.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_i386.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_i386.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_i386.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:i386.
+Unpacking zlib1g-dev:i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_i386.deb) ...
+Setting up libncursesw5:i386 (5.9-10) ...
+Setting up libpipeline1:i386 (1.2.2-1) ...
+Setting up libssl1.0.0:i386 (1.0.1c-4) ...
+Setting up libasprintf0c2:i386 (0.18.1.1-9) ...
+Setting up libmagic1:i386 (5.11-2) ...
+Setting up libpcre3:i386 (1:8.31-1) ...
+Setting up libsqlite3-0:i386 (3.7.14.1-1) ...
+Setting up libxml2:i386 (2.8.0+dfsg1-6) ...
+Setting up libffi5:i386 (3.0.10-3) ...
+Setting up libglib2.0-0:i386 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:i386 (0.6.6-1) ...
+Setting up libexpat1:i386 (2.1.0-1) ...
+Setting up libunistring0:i386 (0.9.3-5) ...
+Setting up libgettextpo0:i386 (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:i386 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.22-5 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_3.2.7-1
-Package versions: apt_0.8.15.9 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 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 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 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_1.4.12-3 gpgv_1.4.12-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 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 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 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_2.2.4-6 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_3.2.7-1 login_1:4.1.5-1 lsb-base_3.2+Debian29 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 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
+Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 libc6-dev_2.13-35 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.5 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libitm1_4.7.2-4 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsigsegv2_2.9-4 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -340,12 +305,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -356,18 +321,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture i386
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -383,11 +348,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -395,30 +360,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -429,7 +396,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -504,7 +471,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -513,7 +480,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -563,10 +530,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -589,6 +559,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -632,7 +603,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -656,7 +627,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -670,6 +641,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -743,16 +715,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
cd debian/bedtools
chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- cd '/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0'
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
@@ -768,77 +762,85 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-i386-baRb9u/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
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
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.16.1-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.17.0-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1252
+Build finished at 20121104-1137
-bedtools_2.16.1-1_i386.changes:
+bedtools_2.17.0-1_i386.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 6fecdcee8b252ddf31ee4c589cd9b48dea74d702 443690 bedtools_2.16.1-1_i386.deb
+ 0468a274169f528f8d6044967ba08a565693e471 448480 bedtools_2.17.0-1_i386.deb
Checksums-Sha256:
- 04d15e827e69504a80711494afe9f4cef5e17ecd7fbb5832bfdede08313555c2 443690 bedtools_2.16.1-1_i386.deb
+ d47a9472f21292f5401fe9f28d7710873f127d9709fdb06a78b0b00a61eda008 448480 bedtools_2.17.0-1_i386.deb
Files:
- 586a70855d6e9d1defb821e8943e02e8 443690 science optional bedtools_2.16.1-1_i386.deb
+ 9664467b070e406eb699d063a429637c 448480 science optional bedtools_2.17.0-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_i386.deb
+bedtools_2.17.0-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 443690 bytes: control archive= 1978 bytes.
- 864 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 448480 bytes: control archive= 4100 bytes.
+ 32 bytes, 1 lines conffiles
+ 832 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1430
- 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)
+ Installed-Size: 1528
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -852,58 +854,168 @@ bedtools_2.16.1-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 36 2012-03-16 12:52 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/bedToBam
--rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/flankBed
--rwxr-xr-x root/root 29 2012-03-16 12:52 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/intersectBed
--rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/subtractBed
--rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/getOverlap
--rwxr-xr-x root/root 1403068 2012-03-16 12:52 ./usr/bin/bedtools
--rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/windowBed
--rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/randomBed
--rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/tagBam
--rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/coverageBed
--rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/mergeBed
--rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/mapBed
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/annotateBed
--rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/closestBed
--rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/pairToPair
--rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/complementBed
--rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 36 2012-03-16 12:52 ./usr/bin/windowMaker
--rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/bamToBed
--rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/pairToBed
--rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/clusterBed
--rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 29 2012-03-16 12:52 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:49 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/bin/
+-rwxr-xr-x root/root 36 2012-11-04 11:37 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1357996 2012-11-04 11:37 ./usr/bin/bedtools
+-rwxr-xr-x root/root 43 2012-11-04 11:37 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 42 2012-11-04 11:37 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 36 2012-11-04 11:37 ./usr/bin/tagBam
+-rwxr-xr-x root/root 44 2012-11-04 11:37 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 36 2012-11-04 11:37 ./usr/bin/nucBed
+-rwxr-xr-x root/root 39 2012-11-04 11:37 ./usr/bin/randomBed
+-rwxr-xr-x root/root 37 2012-11-04 11:37 ./usr/bin/sortBed
+-rwxr-xr-x root/root 39 2012-11-04 11:37 ./usr/bin/windowBed
+-rwxr-xr-x root/root 43 2012-11-04 11:37 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 40 2012-11-04 11:37 ./usr/bin/closestBed
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 42 2012-11-04 11:37 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 44 2012-11-04 11:37 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 40 2012-11-04 11:37 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 42 2012-11-04 11:37 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 38 2012-11-04 11:37 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 43 2012-11-04 11:37 ./usr/bin/complementBed
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 40 2012-11-04 11:37 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 11:37 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 38 2012-11-04 11:37 ./usr/bin/linksBed
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 43 2012-11-04 11:37 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 40 2012-11-04 11:37 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 42 2012-11-04 11:37 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 41 2012-11-04 11:37 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 36 2012-11-04 11:37 ./usr/bin/mapBed
+-rwxr-xr-x root/root 38 2012-11-04 11:37 ./usr/bin/flankBed
+-rwxr-xr-x root/root 42 2012-11-04 11:37 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 37 2012-11-04 11:37 ./usr/bin/slopBed
+-rwxr-xr-x root/root 39 2012-11-04 11:37 ./usr/bin/expandCols
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:37 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -917,26 +1029,96 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-efc38c0f-ecec-4245-8b7f-ce411fa8dba3/build/buildd-bedtools_2.16.1-1-i386-Y60OvV
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-i386-sbuild-657b9628-716f-4fc2-8673-01fbb0424323/build/buildd-bedtools_2.17.0-1-i386-baRb9u
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libasprintf0c2* libcroco3*
+ libexpat1* libffi5* libgettextpo0* libglib2.0-0* libmagic1* libncursesw5*
+ libpcre3* libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2*
+ man-db* mime-support* po-debconf* python* python-minimal* python2.7*
+ python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 33 to remove and 22 not upgraded.
+After this operation, 51.3 MB disk space will be freed.
+(Reading database ... 13442 files and directories currently installed.)
+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 cdbs ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libasprintf0c2:i386 ...
+Removing libcroco3:i386 ...
+Purging configuration files for libcroco3:i386 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libexpat1:i386 ...
+Purging configuration files for libexpat1:i386 ...
+Removing libglib2.0-0:i386 ...
+Purging configuration files for libglib2.0-0:i386 ...
+Removing libffi5:i386 ...
+Purging configuration files for libffi5:i386 ...
+Removing libgettextpo0:i386 ...
+Removing libmagic1:i386 ...
+Purging configuration files for libmagic1:i386 ...
+Removing libncursesw5:i386 ...
+Purging configuration files for libncursesw5:i386 ...
+Removing libpcre3:i386 ...
+Purging configuration files for libpcre3:i386 ...
+Removing libpipeline1:i386 ...
+Purging configuration files for libpipeline1:i386 ...
+Removing libsqlite3-0:i386 ...
+Purging configuration files for libsqlite3-0:i386 ...
+Removing libssl1.0.0:i386 ...
+Purging configuration files for libssl1.0.0:i386 ...
+Removing libunistring0:i386 ...
+Purging configuration files for libunistring0:i386 ...
+Removing libxml2:i386 ...
+Purging configuration files for libxml2:i386 ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
+Removing zlib1g-dev:i386 ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 71588
-Build-Time: 201
+Build-Space: 74760
+Build-Time: 260
Distribution: sid
-Install-Time: 58
-Job: bedtools_2.16.1-1
+Install-Time: 17
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 298
-Source-Version: 2.16.1-1
-Space: 71588
+Package-Time: 291
+Source-Version: 2.17.0-1
+Space: 74760
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1252
-Build needed 00:04:58, 71588k disc space
-Signature with key '6EBCB100' requested:
+Finished at 20121104-1137
+Build needed 00:04:51, 74760k disc space
+Signature with key '2B54027C' requested:
diff --git a/ia64.log b/ia64.log
index d3aeece..ee19247 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,69 +1,68 @@
-From buildd at alkman.debian.org Fri Mar 16 13:26:06 2012
-Return-path: <buildd at alkman.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at caballero.debian.org Sun Nov 04 11:39:35 2012
+Return-path: <buildd at caballero.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1S8XAU-0008CO-L6
- for logs at buildd.debian.org; Fri, 16 Mar 2012 13:26:06 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1TUyYB-0001vh-0p
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:39:35 +0000
+Received: from caballero.debian.org ([193.201.200.200])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1S8XAS-00023V-U3
- for logs at buildd.debian.org; Fri, 16 Mar 2012 13:26:05 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1S8XAQ-0002sS-Pl; Fri, 16 Mar 2012 13:26:02 +0000
-Date: Fri, 16 Mar 2012 13:26:02 +0000
-Message-Id: <E1S8XAQ-0002sS-Pl at alkman.debian.org>
-From: buildd on alkman <buildd at alkman.debian.org>
-To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on ia64 (dist=sid)
+ CN=caballero.debian.org,
+ EMAIL=hostmaster at caballero.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1TUyY9-0005SW-7o; Sun, 04 Nov 2012 11:39:33 +0000
+Received: from buildd by caballero.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at caballero.debian.org>) id 1TUyY8-0005pC-3T
+ for buildd-porters at caballero.debian.org; Sun, 04 Nov 2012 11:39:32 +0000
+Date: Sun, 04 Nov 2012 11:39:32 +0000
+Message-Id: <E1TUyY8-0005pC-3T at caballero.debian.org>
+From: buildd on caballero <buildd at caballero.debian.org>
+To: buildd-porters at caballero.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Delivered-To: buildd-porters at caballero.debian.org
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (ia64) 16 Mar 2012 13:11 ║
+║ bedtools 2.17.0-1 (ia64) 04 Nov 2012 11:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [198 kB]
-Get:2 http://incoming.debian.org unstable InRelease [198 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [6213 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [54.4 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [99.8 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [5659 kB]
+Hit http://ftp.uk.debian.org sid InRelease
+Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [37.4 kB]
-Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2223 B]
-Get:11 http://spohr.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:12 http://spohr.debian.org unstable/main Translation-en [3902 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main ia64 Packages [5659 kB]
-Get:16 http://incoming.debian.org unstable/contrib ia64 Packages [37.4 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [60.0 kB]
-Get:22 http://incoming.debian.org Packages [691 kB]
+Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/main ia64 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/contrib ia64 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/contrib Translation-en/DiffIndex
+Hit http://ftp.uk.debian.org sid/main Translation-en/DiffIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:3 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
+Hit http://incoming.debian.org sid/main Translation-en/DiffIndex
+Get:4 http://incoming.debian.org Release [1141 B]
+Ign http://incoming.debian.org sid/main 2012-11-04-0210.01.pdiff
+Ign http://incoming.debian.org sid/main ia64 2012-11-04-0210.01.pdiff
+Get:5 http://incoming.debian.org Sources [16.2 kB]
+Get:6 http://incoming.debian.org Packages [140 kB]
+Hit http://incoming.debian.org sid/main
+Hit http://incoming.debian.org sid/main ia64
Ign http://incoming.debian.org Translation-en
-Fetched 33.2 MB in 28s (1170 kB/s)
+Fetched 174 kB in 7s (23.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,12 +82,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (873 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (707 kB/s)
Download complete and in download only mode
Check arch
@@ -102,252 +101,94 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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, libc6.1-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
+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, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.2)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.7)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-7)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-28)
+sysvinit: already installed (2.88dsf-28)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6.1-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6.1-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: missing
-Using default version 9.20120312
+debhelper: already installed (9.20120909 >= 9 is satisfied)
quilt: missing
-python: missing
-zlib1g-dev: missing
+python: already installed (2.7.3-1)
+zlib1g-dev: already installed (1:1.2.7.dfsg-13)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
+Installing positive dependencies: cdbs quilt
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ diffstat
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl python-doc python-tk python2.7-doc
- binfmt-support procmail graphviz default-mta mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ devscripts procmail graphviz default-mta mail-transport-agent
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 50 not upgraded.
-Need to get 21.3 MB of archives.
-After this operation, 66.6 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main zlib1g ia64 1:1.2.6.dfsg-2 [117 kB]
-Get:2 http://spohr.debian.org/debian/ unstable/main libncursesw5 ia64 5.9-4 [387 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.1-1 [48.2 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main libssl1.0.0 ia64 1.0.0h-1 [1565 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.10-1 [274 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main libffi5 ia64 3.0.10-3 [35.5 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.30.2-6 [2198 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-7 [1179 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.4-2 [174 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libexpat1 ia64 2.0.1-7.2 [212 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main libdb4.8 ia64 4.8.30-11 [1117 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 9.0.1 [240 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.1-1 [1156 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main file ia64 5.10-1 [55.2 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
-Get:19 http://spohr.debian.org/debian/ unstable/main libsqlite3-0 ia64 3.7.10-1 [639 kB]
-Get:20 http://spohr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://spohr.debian.org/debian/ unstable/main python2.7-minimal ia64 2.7.3~rc1-1 [2192 kB]
-Get:22 http://spohr.debian.org/debian/ unstable/main python2.7 ia64 2.7.3~rc1-1 [2892 kB]
-Get:23 http://spohr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://spohr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:26 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:27 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 kB]
-Get:28 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:29 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://spohr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.55-2 [37.2 kB]
-Get:32 http://spohr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.6.dfsg-2 [251 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 21.3 MB in 8s (2576 kB/s)
-(Reading database ... 10668 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_ia64.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10668 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_ia64.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_ia64.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_ia64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_ia64.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_ia64.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_ia64.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_ia64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_ia64.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_ia64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_ia64.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_ia64.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_ia64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_ia64.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_ia64.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_ia64.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_ia64.deb) ...
-Selecting previously unselected package mime-support.
-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_2.7.3~rc1-1_ia64.deb) ...
-Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_ia64.deb) ...
-Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
-Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+ cdbs diffstat quilt
+0 upgraded, 3 newly installed, 0 to remove and 89 not upgraded.
+Need to get 0 B/495 kB of archives.
+After this operation, 1200 kB of additional disk space will be used.
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_ia64.deb) ...
-Selecting previously unselected package intltool-debian.
-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_9.20120312_all.deb) ...
+(Reading database ... 28133 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_ia64.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_ia64.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_ia64.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
-No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
-Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.118) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6.1-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.2-1
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -358,12 +199,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -374,18 +215,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture ia64
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 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -401,11 +242,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -413,30 +254,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -447,7 +290,7 @@ CURRENT_VERSION = v2.16.1
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -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
@@ -526,7 +369,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -535,7 +378,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -585,10 +428,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -611,6 +457,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -654,7 +501,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -678,7 +525,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -692,6 +539,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -765,16 +613,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
cd debian/bedtools
- chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- cd '/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+ 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 '/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0'
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
@@ -790,77 +660,86 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-ia64-mSVWnX/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
+dh_girepository -pbedtools
+ rm -f
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.16.1-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../bedtools_2.17.0-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1325
+Build finished at 20121104-1139
-bedtools_2.16.1-1_ia64.changes:
+bedtools_2.17.0-1_ia64.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
+Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 5fe4f50408eb6aecaca594ed2df7c32e364b66d5 554952 bedtools_2.16.1-1_ia64.deb
+ 3bcf36fabe68935cc660f121a4f232747089f792 574956 bedtools_2.17.0-1_ia64.deb
Checksums-Sha256:
- b7c2679048e1719d8f4e56902ea5d493d90ee47823566d41531b6e6cc376b3e5 554952 bedtools_2.16.1-1_ia64.deb
+ 7c3b6b390baf728866dd64e2fa3fb2a6dc7343adf63f61a141342bb06394dc36 574956 bedtools_2.17.0-1_ia64.deb
Files:
- 54491056fab0589c0e567a0aed56235f 554952 science optional bedtools_2.16.1-1_ia64.deb
+ d6e2d1b1728ade6201caaaff86290b03 574956 science optional bedtools_2.17.0-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_ia64.deb
+bedtools_2.17.0-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 554952 bytes: control archive= 1984 bytes.
- 878 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 574956 bytes: control archive= 4115 bytes.
+ 32 bytes, 1 lines conffiles
+ 846 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 2904
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6.1 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
+ Installed-Size: 3132
+ Depends: libc6.1 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), libunwind7, zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -874,58 +753,168 @@ bedtools_2.16.1-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 13:25 ./
-drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/bin/
--rwxr-xr-x root/root 2947432 2012-03-16 13:25 ./usr/bin/bedtools
--rwxr-xr-x root/root 36 2012-03-16 13:25 ./usr/bin/windowMaker
--rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/windowBed
--rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/tagBam
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/subtractBed
--rwxr-xr-x root/root 29 2012-03-16 13:25 ./usr/bin/sortBed
--rwxr-xr-x root/root 29 2012-03-16 13:25 ./usr/bin/slopBed
--rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/randomBed
--rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/pairToPair
--rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/pairToBed
--rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/nucBed
--rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/mergeBed
--rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/mapBed
--rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/intersectBed
--rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/flankBed
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/coverageBed
--rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/complementBed
--rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/clusterBed
--rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/closestBed
--rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/bedToBam
--rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 36 2012-03-16 13:25 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/bamToBed
--rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/annotateBed
-drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/bedtools/
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+-rwxr-xr-x root/root 43 2012-11-04 11:39 ./usr/bin/pairToPair
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+-rwxr-xr-x root/root 37 2012-11-04 11:39 ./usr/bin/sortBed
+-rwxr-xr-x root/root 41 2012-11-04 11:39 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-11-04 11:39 ./usr/bin/tagBam
+-rwxr-xr-x root/root 42 2012-11-04 11:39 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 39 2012-11-04 11:39 ./usr/bin/windowBed
+-rwxr-xr-x root/root 44 2012-11-04 11:39 ./usr/bin/windowMaker
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+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -939,27 +928,42 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-63cdf3bb-1ec5-4067-923f-5e97de6f9b23/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-3bbca110-4cb3-4694-a4e6-de94777c3b7a/build/buildd-bedtools_2.17.0-1-ia64-mSVWnX
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* diffstat* quilt*
+0 upgraded, 0 newly installed, 3 to remove and 89 not upgraded.
+After this operation, 1200 kB disk space will be freed.
+(Reading database ... 28268 files and directories currently installed.)
+Removing cdbs ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 138532
-Build-Time: 681
+Build-Space: 134348
+Build-Time: 639
Distribution: sid
-Install-Time: 111
-Job: bedtools_2.16.1-1
+Install-Time: 14
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 856
-Source-Version: 2.16.1-1
-Space: 138532
+Package-Time: 674
+Source-Version: 2.17.0-1
+Space: 134348
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1325
-Build needed 00:14:16, 138532k disc space
-Signature with key '94AE7BC0' requested:
+Finished at 20121104-1139
+Build needed 00:11:14, 134348k disc space
diff --git a/info b/info
index 716bd80..1fb46e1 100644
--- a/info
+++ b/info
@@ -1,13 +1,13 @@
-s390x~1331900322~sid~successful
-kfreebsd-i386~1331900511~sid~successful
-s390~1331900808~sid~successful
-hurd-i386~1331901235~sid~successful
-mipsel~1331901700~sid~successful
-i386~1331902380~sid~successful
-armel~1331902487~sid~successful
-mips~1331902619~sid~successful
-ia64~1331904367~sid~successful
-sparc~1331905264~sid~successful
-armhf~1331906656~sid~successful
-powerpc~1331907608~sid~successful
-kfreebsd-amd64~1331917049~sid~successful
+s390~1352028830~sid~successful
+powerpc~1352028937~sid~successful
+kfreebsd-i386~1352028945~sid~successful
+s390x~1352028994~sid~successful
+i386~1352029059~sid~successful
+kfreebsd-amd64~1352029118~sid~successful
+ia64~1352029175~sid~successful
+sparc~1352029553~sid~successful
+mipsel~1352030115~sid~successful
+mips~1352030175~sid~successful
+armhf~1352030268~sid~successful
+armel~1352030522~sid~successful
+hurd-i386~1352037329~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 550984e..8a80b47 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,78 +1,62 @@
-From buildd at fasch.debian.org Fri Mar 16 16:57:26 2012
-Return-path: <buildd at fasch.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at fano.debian.org Sun Nov 04 11:38:38 2012
+Return-path: <buildd at fano.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
- id 1S8aSz-0004xK-St
- for logs at buildd.debian.org; Fri, 16 Mar 2012 16:57:26 +0000
-Received: from fasch.debian.org ([194.177.211.201])
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1TUyXG-0001lj-8O
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:38:38 +0000
+Received: from fano.debian.org ([206.12.19.110])
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- CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
- id 1S8aSx-0001Ma-Q2; Fri, 16 Mar 2012 16:57:24 +0000
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-Message-Id: <E1S8aSw-0001pb-RJ at fasch.debian.org>
+ CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+ id 1TUyXC-000PiZ-8w; Sun, 04 Nov 2012 11:38:34 +0000
+Message-Id: <E1TUyXC-000PiZ-8w at fano.debian.org>
MIME-Version: 1.0
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-Date: Fri, 16 Mar 2012 16:57:22 +0000
-From: buildd on fasch <buildd at fasch.debian.org>
-To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on kfreebsd-amd64
+Date: Sun, 4 Nov 2012 11:38:34 +0000
+From: buildd on fano <buildd at fano.debian.org>
+To: logs at buildd.debian.org,christoph at debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 94C0145B
+Key-Id: 4584BE29
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (kfreebsd-amd64) 16 Mar 2012 16:49 ║
+║ bedtools 2.17.0-1 (kfreebsd-amd64) 04 Nov 2012 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: kfreebsd-amd64
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org unstable InRelease [219 kB]
+Get:2 http://mirror-ubc.debian.org unstable InRelease [219 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6381 kB]
+Get:4 http://mirror-ubc.debian.org unstable/contrib Sources [53.1 kB]
+Get:5 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:6 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5717 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release.gpg
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://ftp.gr.debian.org sid/contrib Translation-en
-Hit http://ftp.gr.debian.org sid/main Translation-en
-Hit http://ftp.gr.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://incoming.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Translation-en
-Hit http://incoming.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org Translation-en
+Get:7 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [36.5 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5717 kB]
+Get:12 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [36.5 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.2 MB in 49s (512 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -92,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 0s (6627 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 2s (563 kB/s)
Download complete and in download only mode
Check arch
@@ -111,58 +95,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.7)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3.1)
+base-files: already installed (6.12)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-2)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
-findutils: already installed (4.4.2-4)
-freebsd-utils: already installed (9.0-2)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+freebsd-utils: already installed (9.0+ds1-8)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.5-1)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-4)
-util-linux: already installed (2.20.1-4)
+bsdutils: already installed (1:2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -173,9 +157,9 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
- libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
- python-minimal python2.7 python2.7-minimal
+ libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
+ libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2
+ man-db mime-support po-debconf python-minimal python2.7 python2.7-minimal
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
python-doc python-tk python2.7-doc binfmt-support procmail graphviz
@@ -185,111 +169,148 @@ Recommended packages:
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1
- libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
- mime-support po-debconf python python-minimal python2.7 python2.7-minimal
- quilt zlib1g-dev
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python python-minimal python2.7
+ python2.7-minimal quilt zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 1 not upgraded.
+Need to get 16.3 MB of archives.
+After this operation, 44.4 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 kfreebsd-amd64 5.9-10 [140 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.2-1 [39.8 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libssl1.0.0 kfreebsd-amd64 1.0.1c-4 [1215 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-9 [26.8 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 5.11-2 [202 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 kfreebsd-amd64 3.7.14.1-1 [457 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-6 [914 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.33.12+really2.32.4-3 [1831 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.6-1 [133 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-9 [145 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.21-9 [1113 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.3-1 [1053 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 5.11-2 [51.8 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-9 [153 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main python2.7-minimal kfreebsd-amd64 2.7.3-5 [1695 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main python2.7 kfreebsd-amd64 2.7.3-5 [2667 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-9 [1965 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:30 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/16.7 MB of archives.
-After this operation, 45.2 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1.
-(Reading database ... 11499 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-amd64.deb) ...
+Fetched 16.3 MB in 5s (2816 kB/s)
+Selecting previously unselected package libncursesw5:kfreebsd-amd64.
+(Reading database ... 11630 files and directories currently installed.)
+Unpacking libncursesw5:kfreebsd-amd64 (from .../libncursesw5_5.9-10_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libpipeline1:kfreebsd-amd64.
+Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.2-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libssl1.0.0:kfreebsd-amd64.
+Unpacking libssl1.0.0:kfreebsd-amd64 (from .../libssl1.0.0_1.0.1c-4_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
+Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-9_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libmagic1:kfreebsd-amd64.
+Unpacking libmagic1:kfreebsd-amd64 (from .../libmagic1_5.11-2_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libsqlite3-0:kfreebsd-amd64.
+Unpacking libsqlite3-0:kfreebsd-amd64 (from .../libsqlite3-0_3.7.14.1-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libxml2:kfreebsd-amd64.
+Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-6_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libffi5:kfreebsd-amd64.
+Unpacking libffi5:kfreebsd-amd64 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
+Unpacking libglib2.0-0:kfreebsd-amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-3_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libcroco3:kfreebsd-amd64.
+Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.6-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libunistring0:kfreebsd-amd64.
+Unpacking libunistring0:kfreebsd-amd64 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libgettextpo0:kfreebsd-amd64.
+Unpacking libgettextpo0:kfreebsd-amd64 (from .../libgettextpo0_0.18.1.1-9_kfreebsd-amd64.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_kfreebsd-amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.10-1_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_5.11-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_kfreebsd-amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_kfreebsd-amd64.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_kfreebsd-amd64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-11_kfreebsd-amd64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_kfreebsd-amd64.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-amd64.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_kfreebsd-amd64.deb) ...
-Setting up libpipeline1 (1.2.1-1) ...
-Setting up libssl1.0.0 (1.0.0h-1) ...
-Setting up libmagic1 (5.10-1) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
+Unpacking zlib1g-dev:kfreebsd-amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-amd64.deb) ...
+Setting up libncursesw5:kfreebsd-amd64 (5.9-10) ...
+Setting up libpipeline1:kfreebsd-amd64 (1.2.2-1) ...
+Setting up libssl1.0.0:kfreebsd-amd64 (1.0.1c-4) ...
+Setting up libasprintf0c2:kfreebsd-amd64 (0.18.1.1-9) ...
+Setting up libmagic1:kfreebsd-amd64 (5.11-2) ...
+Setting up libsqlite3-0:kfreebsd-amd64 (3.7.14.1-1) ...
+Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-6) ...
+Setting up libffi5:kfreebsd-amd64 (3.0.10-3) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-7) ...
-Setting up libcroco3 (0.6.4-2) ...
-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 (2.6.1-1) ...
+Setting up libcroco3:kfreebsd-amd64 (0.6.6-1) ...
+Setting up libunistring0:kfreebsd-amd64 (0.9.3-5) ...
+Setting up libgettextpo0:kfreebsd-amd64 (0.18.1.1-9) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.2-11) ...
-Setting up python2.7 (2.7.2-11) ...
-Setting up python-minimal (2.7.2-10) ...
-Setting up python (2.7.2-10) ...
-Setting up cdbs (0.4.109) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-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 kfreebsd-kernel-headers_0.77 libc0.1-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1
-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 freebsd-utils_9.0-2 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 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 kbdcontrol_9.0-2 kfreebsd-kernel-headers_0.77 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbsd0_0.3.0-2 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc0.1_2.13-27 libc0.1-dev_2.13-27 libcam6_9.0+ds1-1 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 libgeom1_9.0+ds1-1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 libgssglue1_0.3-4 libjail1_9.0+ds1-1 libkiconv4_9.0+ds1-1 libkvm0_9.0+ds1-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 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 libprocps0_1:3.3.2-3 libquadmath0_4.6.3-1 libreadline6_6.2-8 libsbuf6_9.0+ds1-1 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 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 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 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 procps_1:3.3.2-3 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-8 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 type-handling_0.2.23 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
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf0c2_0.18.1.1-9 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc0.1_2.13-36 libc0.1-dev_2.13-36 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -300,12 +321,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -316,18 +337,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture kfreebsd-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -343,11 +364,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -355,30 +376,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -389,7 +412,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -417,6 +440,8 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling BamWriter_p.cpp
* compiling BamIndexFactory_p.cpp
* compiling BamStandardIndex_p.cpp
+src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)':
+src/api/internal/index/BamStandardIndex_p.cpp:958:89: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling BamToolsIndex_p.cpp
* compiling BamDeviceFactory_p.cpp
* compiling BamFile_p.cpp
@@ -468,7 +493,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -477,7 +502,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -527,10 +552,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -553,6 +581,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -596,7 +625,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -620,7 +649,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -634,6 +663,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -707,16 +737,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0'
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
@@ -732,8 +784,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -743,66 +798,70 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../bedtools_2.16.1-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.17.0-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1656
+Build finished at 20121104-1138
-bedtools_2.16.1-1_kfreebsd-amd64.changes:
+bedtools_2.17.0-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- d966edbb0e68c00d12945145593d9e9341b33e25 434400 bedtools_2.16.1-1_kfreebsd-amd64.deb
+ d017bfbed27b5e6dd38e41556d7d5d75a8e33796 442880 bedtools_2.17.0-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 9939dca6f2b649229d993e6fae23ed47179f1f0ad4eb86da6bd3f9379ccf3d36 434400 bedtools_2.16.1-1_kfreebsd-amd64.deb
+ eb59d98850f419a686626e8acb1f2d5a1be348b377f4dbf12960bbeaa25007d3 442880 bedtools_2.17.0-1_kfreebsd-amd64.deb
Files:
- 1afb73612304e7654b53fbf558eea4c4 434400 science optional bedtools_2.16.1-1_kfreebsd-amd64.deb
+ 4550a3a1693fd465bffd4038052c64a0 442880 science optional bedtools_2.17.0-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_kfreebsd-amd64.deb
+bedtools_2.17.0-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 434400 bytes: control archive= 1983 bytes.
- 876 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 442880 bytes: control archive= 4116 bytes.
+ 32 bytes, 1 lines conffiles
+ 844 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1385
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1417
+ Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -816,58 +875,168 @@ bedtools_2.16.1-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 16:52 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 16:55 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/bedToBam
--rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 1388184 2012-03-16 16:55 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/coverageBed
--rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/flankBed
--rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/intersectBed
--rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/mapBed
--rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/pairToBed
--rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/pairToPair
--rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 29 2012-03-16 16:55 ./usr/bin/slopBed
--rwxr-xr-x root/root 29 2012-03-16 16:55 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/tagBam
--rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-03-16 16:55 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:34 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./usr/bin/
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:38 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 44 2012-11-04 11:38 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 43 2012-11-04 11:38 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-11-04 11:38 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1351312 2012-11-04 11:38 ./usr/bin/bedtools
+-rwxr-xr-x root/root 40 2012-11-04 11:38 ./usr/bin/closestBed
+-rwxr-xr-x root/root 40 2012-11-04 11:38 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 11:38 ./usr/bin/complementBed
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 39 2012-11-04 11:38 ./usr/bin/expandCols
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:38 ./usr/bin/flankBed
+-rwxr-xr-x root/root 42 2012-11-04 11:38 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 40 2012-11-04 11:38 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 42 2012-11-04 11:38 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 38 2012-11-04 11:38 ./usr/bin/linksBed
+-rwxr-xr-x root/root 36 2012-11-04 11:38 ./usr/bin/mapBed
+-rwxr-xr-x root/root 42 2012-11-04 11:38 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:38 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 43 2012-11-04 11:38 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 36 2012-11-04 11:38 ./usr/bin/nucBed
+-rwxr-xr-x root/root 42 2012-11-04 11:38 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:38 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 39 2012-11-04 11:38 ./usr/bin/randomBed
+-rwxr-xr-x root/root 40 2012-11-04 11:38 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 37 2012-11-04 11:38 ./usr/bin/slopBed
+-rwxr-xr-x root/root 37 2012-11-04 11:38 ./usr/bin/sortBed
+-rwxr-xr-x root/root 41 2012-11-04 11:38 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-11-04 11:38 ./usr/bin/tagBam
+-rwxr-xr-x root/root 42 2012-11-04 11:38 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 39 2012-11-04 11:38 ./usr/bin/windowBed
+-rwxr-xr-x root/root 44 2012-11-04 11:38 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:38 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -881,86 +1050,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1331916571-2471/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0*
- libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2*
- man-db* mime-support* po-debconf* python* python-minimal* python2.7*
- python2.7-minimal* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 28 to remove and 0 not upgraded.
-After this operation, 45.2 MB disk space will be freed.
-(Reading database ... 13771 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing python ...
-Purging configuration files for python ...
-Removing python2.7 ...
-Purging configuration files for python2.7 ...
-Removing libdb4.8 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
-Removing python-minimal ...
-Removing python2.7-minimal ...
-Purging configuration files for python2.7-minimal ...
-Removing libssl1.0.0 ...
-Purging configuration files for libssl1.0.0 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing mime-support ...
-Purging configuration files for mime-support ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1352028639-94706/build/buildd-bedtools_2.17.0-1-kfreebsd-amd64-LPHYsW
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 118126
-Build-Time: 232
+Build-Space: 118942
+Build-Time: 229
Distribution: sid
-Install-Time: 132
-Job: bedtools_2.16.1-1
+Install-Time: 76
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 389
-Source-Version: 2.16.1-1
-Space: 118126
+Package-Time: 471
+Source-Version: 2.17.0-1
+Space: 118942
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1656
-Build needed 00:06:29, 118126k disc space
-Signature with key '94C0145B' requested:
+Finished at 20121104-1138
+Build needed 00:07:51, 118942k disc space
+Signature with key '4584BE29' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index f615341..491421c 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,76 +1,62 @@
-From buildd at finzi.debian.org Fri Mar 16 12:21:51 2012
+From buildd at finzi.debian.org Sun Nov 04 11:35:45 2012
Return-path: <buildd at finzi.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1S8WAI-0002fV-VJ
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:21:51 +0000
+ id 1TUyUT-0001Ig-4n
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:35:45 +0000
Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1S8WAH-0005LH-PB; Fri, 16 Mar 2012 12:21:50 +0000
+ id 1TUyUR-00059S-AT; Sun, 04 Nov 2012 11:35:44 +0000
Received: from buildd by finzi.debian.org with local (Exim 4.72)
(envelope-from <buildd at finzi.debian.org>)
- id 1S8WAF-000KXY-3E; Fri, 16 Mar 2012 12:21:47 +0000
-Message-Id: <E1S8WAF-000KXY-3E at finzi.debian.org>
+ id 1TUyUP-000LBZ-1b; Sun, 04 Nov 2012 11:35:41 +0000
+Message-Id: <E1TUyUP-000LBZ-1b at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 12:21:46 +0000
+Date: Sun, 4 Nov 2012 11:35:40 +0000
From: buildd on finzi <buildd at finzi.debian.org>
-To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on kfreebsd-i386
+To: logs at buildd.debian.org,christoph at debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on kfreebsd-i386
(dist=sid)
-Key-Id: 76BB3C42
+Key-Id: B3DA9773
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (kfreebsd-i386) 16 Mar 2012 12:16 ║
+║ bedtools 2.17.0-1 (kfreebsd-i386) 04 Nov 2012 11:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: kfreebsd-i386
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org unstable InRelease [219 kB]
Ign http://incoming.debian.org InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org Release.gpg
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://mirror-ubc.debian.org sid/contrib Translation-en
-Hit http://mirror-ubc.debian.org sid/main Translation-en
-Hit http://mirror-ubc.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Translation-en
-Hit http://incoming.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org Translation-en
+Get:2 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:3 http://mirror-ubc.debian.org unstable InRelease [219 kB]
+Get:4 http://mirror-ubc.debian.org unstable/main Sources [6381 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.1 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5715 kB]
+Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5715 kB]
+Get:12 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.2 MB in 17s (1480 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (640 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (710 kB/s)
Download complete and in download only mode
Check arch
@@ -109,58 +95,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.7)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3.1)
+base-files: already installed (6.12)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-2)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
-findutils: already installed (4.4.2-4)
-freebsd-utils: already installed (9.0-2)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+freebsd-utils: already installed (9.0+ds1-8)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.5-1)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-4)
-util-linux: already installed (2.20.1-4)
+bsdutils: already installed (1:2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -170,120 +156,172 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
- libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
- python-minimal python2.7 python2.7-minimal
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python-minimal
+ python2.7 python2.7-minimal
Suggested packages:
- devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
- python-doc python-tk python2.7-doc binfmt-support procmail graphviz
- default-mta mail-transport-agent
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 16.5 MB of archives.
+After this operation, 44.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 kfreebsd-i386 5.9-10 [147 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.2-1 [38.8 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libssl1.0.0 kfreebsd-i386 1.0.1c-4 [1192 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-9 [26.7 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.31-1 [247 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 kfreebsd-i386 3.7.14.1-1 [465 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-6 [904 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.33.12+really2.32.4-3 [1819 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.6-1 [133 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-9 [140 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.3-1 [1038 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-9 [131 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main python2.7-minimal kfreebsd-i386 2.7.3-5 [1647 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main python2.7 kfreebsd-i386 2.7.3-5 [2636 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-9 [1894 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:30 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
+Get:31 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:32 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/15.4 MB of archives.
-After this operation, 41.3 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1.
-(Reading database ... 11923 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_kfreebsd-i386.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_kfreebsd-i386.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_kfreebsd-i386.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-i386.deb) ...
+Fetched 16.5 MB in 4s (3989 kB/s)
+Selecting previously unselected package libncursesw5:kfreebsd-i386.
+(Reading database ... 11298 files and directories currently installed.)
+Unpacking libncursesw5:kfreebsd-i386 (from .../libncursesw5_5.9-10_kfreebsd-i386.deb) ...
+Selecting previously unselected package libpipeline1:kfreebsd-i386.
+Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.2-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libssl1.0.0:kfreebsd-i386.
+Unpacking libssl1.0.0:kfreebsd-i386 (from .../libssl1.0.0_1.0.1c-4_kfreebsd-i386.deb) ...
+Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
+Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-9_kfreebsd-i386.deb) ...
+Selecting previously unselected package libmagic1:kfreebsd-i386.
+Unpacking libmagic1:kfreebsd-i386 (from .../libmagic1_5.11-2_kfreebsd-i386.deb) ...
+Selecting previously unselected package libpcre3:kfreebsd-i386.
+Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.31-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libsqlite3-0:kfreebsd-i386.
+Unpacking libsqlite3-0:kfreebsd-i386 (from .../libsqlite3-0_3.7.14.1-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libxml2:kfreebsd-i386.
+Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-6_kfreebsd-i386.deb) ...
+Selecting previously unselected package libffi5:kfreebsd-i386.
+Unpacking libffi5:kfreebsd-i386 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
+Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
+Unpacking libglib2.0-0:kfreebsd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_kfreebsd-i386.deb) ...
+Selecting previously unselected package libcroco3:kfreebsd-i386.
+Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.6-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libunistring0:kfreebsd-i386.
+Unpacking libunistring0:kfreebsd-i386 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package libgettextpo0:kfreebsd-i386.
+Unpacking libgettextpo0:kfreebsd-i386 (from .../libgettextpo0_0.18.1.1-9_kfreebsd-i386.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_kfreebsd-i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.10-1_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_5.11-2_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-i386.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_kfreebsd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_kfreebsd-i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_kfreebsd-i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_kfreebsd-i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-11_kfreebsd-i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_kfreebsd-i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_kfreebsd-i386.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-i386.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_kfreebsd-i386.deb) ...
-Setting up libpipeline1 (1.2.1-1) ...
-Setting up libssl1.0.0 (1.0.0h-1) ...
-Setting up libmagic1 (5.10-1) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
+Unpacking zlib1g-dev:kfreebsd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-i386.deb) ...
+Setting up libncursesw5:kfreebsd-i386 (5.9-10) ...
+Setting up libpipeline1:kfreebsd-i386 (1.2.2-1) ...
+Setting up libssl1.0.0:kfreebsd-i386 (1.0.1c-4) ...
+Setting up libasprintf0c2:kfreebsd-i386 (0.18.1.1-9) ...
+Setting up libmagic1:kfreebsd-i386 (5.11-2) ...
+Setting up libpcre3:kfreebsd-i386 (1:8.31-1) ...
+Setting up libsqlite3-0:kfreebsd-i386 (3.7.14.1-1) ...
+Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-6) ...
+Setting up libffi5:kfreebsd-i386 (3.0.10-3) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-7) ...
-Setting up libcroco3 (0.6.4-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up libdb4.8 (4.8.30-11) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:kfreebsd-i386 (0.6.6-1) ...
+Setting up libunistring0:kfreebsd-i386 (0.9.3-5) ...
+Setting up libgettextpo0:kfreebsd-i386 (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.2-11) ...
-Setting up python2.7 (2.7.2-11) ...
-Setting up python-minimal (2.7.2-10) ...
-Setting up python (2.7.2-10) ...
-Setting up cdbs (0.4.109) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-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 kfreebsd-kernel-headers_0.77 libc0.1-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1
-Package versions: apt_0.8.15.10 autotools-dev_20120210.1 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 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.42 debconf-english_1.5.38 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 freebsd-utils_9.0-2 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 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 kbdcontrol_9.0-2 kfreebsd-kernel-headers_0.77 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbsd0_0.3.0-2 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc0.1_2.13-27 libc0.1-dev_2.13-27 libcam6_9.0+ds1-1 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 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_9.0+ds1-1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgnutls26_2.12.17-2 libgomp1_4.6.3-1 libgpg-error0_1.10-3 libgssglue1_0.3-4 libjail1_9.0+ds1-1 libkiconv4_9.0+ds1-1 libkvm0_9.0+ds1-1 libldap-2.4-2_2.4.28-1.1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.12-2 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 libprocps0_1:3.3.2-3 libquadmath0_4.6.3-1 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-4 libsbuf6_9.0+ds1-1 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 libtasn1-3_2.11-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 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 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 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 procps_1:3.3.2-3 psmisc_22.16-1 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 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
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf0c2_0.18.1.1-9 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc0.1_2.13-36 libc0.1-dev_2.13-36 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -294,12 +332,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -310,18 +348,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture kfreebsd-i386
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -337,11 +375,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -349,30 +387,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -383,7 +423,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -458,7 +498,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -467,7 +507,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -517,10 +557,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -543,6 +586,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -586,7 +630,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -610,7 +654,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -624,6 +668,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -697,16 +742,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0'
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
@@ -722,8 +789,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -733,27 +803,27 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.16.1-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.17.0-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1221
+Build finished at 20121104-1135
-bedtools_2.16.1-1_kfreebsd-i386.changes:
+bedtools_2.17.0-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
@@ -761,38 +831,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- cf2e5fce429856d71a47d218357533895a43b37b 443250 bedtools_2.16.1-1_kfreebsd-i386.deb
+ a580021ac7a012cc99441d883d77ef4b8bb477c0 448668 bedtools_2.17.0-1_kfreebsd-i386.deb
Checksums-Sha256:
- 1f77d3f0574b1bb4bbe95831613804b2d8e50948f6adb8cba0ae541fa044855e 443250 bedtools_2.16.1-1_kfreebsd-i386.deb
+ 0c44224ca9cace394e17afd82561b8ce67f9b21a1196f70df7904bc3a6e5ed57 448668 bedtools_2.17.0-1_kfreebsd-i386.deb
Files:
- 7925cc91df148cd76bc4e20158d68c93 443250 science optional bedtools_2.16.1-1_kfreebsd-i386.deb
+ f4cfed76ebb99b21e044f01301f9ef05 448668 science optional bedtools_2.17.0-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_kfreebsd-i386.deb
+bedtools_2.17.0-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 443250 bytes: control archive= 1981 bytes.
- 875 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 448668 bytes: control archive= 4119 bytes.
+ 32 bytes, 1 lines conffiles
+ 843 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1399
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1423
+ Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -806,58 +880,168 @@ bedtools_2.16.1-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:17 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 12:21 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/bedToBam
--rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 1403068 2012-03-16 12:21 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/coverageBed
--rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/flankBed
--rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/intersectBed
--rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/mapBed
--rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/pairToBed
--rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/pairToPair
--rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 29 2012-03-16 12:21 ./usr/bin/slopBed
--rwxr-xr-x root/root 29 2012-03-16 12:21 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/tagBam
--rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-03-16 12:21 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/bin/
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 44 2012-11-04 11:35 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1357996 2012-11-04 11:35 ./usr/bin/bedtools
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/closestBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/complementBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/expandCols
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/flankBed
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/linksBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/mapBed
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/nucBed
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/randomBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 37 2012-11-04 11:35 ./usr/bin/slopBed
+-rwxr-xr-x root/root 37 2012-11-04 11:35 ./usr/bin/sortBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/tagBam
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/windowBed
+-rwxr-xr-x root/root 44 2012-11-04 11:35 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -871,84 +1055,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1331900161-75362/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0* libmagic1*
- libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db*
- mime-support* po-debconf* python* python-minimal* python2.7*
- python2.7-minimal* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 27 to remove and 0 not upgraded.
-After this operation, 41.3 MB disk space will be freed.
-(Reading database ... 14015 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing python ...
-Purging configuration files for python ...
-Removing python2.7 ...
-Purging configuration files for python2.7 ...
-Removing libdb4.8 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
-Removing python-minimal ...
-Removing python2.7-minimal ...
-Purging configuration files for python2.7-minimal ...
-Removing libssl1.0.0 ...
-Purging configuration files for libssl1.0.0 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing mime-support ...
-Purging configuration files for mime-support ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1352028575-77249/build/buildd-bedtools_2.17.0-1-kfreebsd-i386-CSLuXL
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 72048
-Build-Time: 235
+Build-Space: 74924
+Build-Time: 244
Distribution: sid
-Install-Time: 59
-Job: bedtools_2.16.1-1
+Install-Time: 52
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 315
-Source-Version: 2.16.1-1
-Space: 72048
+Package-Time: 358
+Source-Version: 2.17.0-1
+Space: 74924
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1221
-Build needed 00:05:15, 72048k disc space
-Signature with key '76BB3C42' requested:
+Finished at 20121104-1135
+Build needed 00:05:58, 74924k disc space
+Signature with key 'B3DA9773' requested:
diff --git a/mips.log b/mips.log
index 71a90c8..430392e 100644
--- a/mips.log
+++ b/mips.log
@@ -1,69 +1,60 @@
-From buildd2 at corelli.debian.org Fri Mar 16 12:56:52 2012
-Return-path: <buildd2 at corelli.debian.org>
+From buildd at ball.debian.org Sun Nov 04 11:56:15 2012
+Return-path: <buildd at ball.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
- id 1S8WiB-0003Ss-UL
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:52 +0000
-Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1TUyoJ-0004cZ-2I
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:56:15 +0000
+Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
+ CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
- id 1S8WiA-0008L9-8R
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:51 +0000
-Received: from buildd2 by corelli.debian.org with local (Exim 4.72)
- (envelope-from <buildd2 at corelli.debian.org>) id 1S8Wi6-0007Fp-SG
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:47 +0000
-Date: Fri, 16 Mar 2012 12:56:46 +0000
-Message-Id: <E1S8Wi6-0007Fp-SG at corelli.debian.org>
-From: buildd on corelli <buildd2 at corelli.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on mips (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1TUyoH-00077U-Rt
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:56:14 +0000
+Received: from buildd by ball.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at ball.debian.org>)
+ id 1TUyoG-0005ik-D0; Sun, 04 Nov 2012 11:56:12 +0000
+Date: Sun, 04 Nov 2012 11:56:12 +0000
+Message-Id: <E1TUyoG-0005ik-D0 at ball.debian.org>
+From: buildd on ball <buildd at ball.debian.org>
+To: logs at buildd.debian.org,buildd-porters at ball.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (mips) 16 Mar 2012 12:13 ║
+║ bedtools 2.17.0-1 (mips) 04 Nov 2012 11:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [198 kB]
-Get:2 http://incoming.debian.org unstable InRelease [198 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6213 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [219 kB]
+Get:2 http://incoming.debian.org unstable InRelease [219 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [6381 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1616 B]
-Get:6 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [54.4 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [99.8 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main mips Packages [5732 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [37.3 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2223 B]
-Get:12 http://mirror-ubc.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:13 http://mirror-ubc.debian.org unstable/main Translation-en [3902 kB]
-Get:14 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:15 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:16 http://incoming.debian.org unstable/main mips Packages [5732 kB]
-Get:17 http://incoming.debian.org unstable/contrib mips Packages [37.3 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:18 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:19 http://incoming.debian.org Sources [58.9 kB]
-Get:20 http://incoming.debian.org Packages [687 kB]
-Get:21 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:22 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.3 MB in 1min 23s (399 kB/s)
+Get:4 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:5 http://ftp.de.debian.org unstable/contrib Sources [53.1 kB]
+Get:6 http://ftp.de.debian.org unstable/non-free Sources [101 kB]
+Get:7 http://ftp.de.debian.org unstable/main mips Packages [5997 kB]
+Get:8 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:9 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:10 http://incoming.debian.org unstable/main mips Packages [5997 kB]
+Get:11 http://incoming.debian.org unstable/contrib mips Packages [37.3 kB]
+Get:12 http://incoming.debian.org Release.gpg [836 B]
+Get:13 http://incoming.debian.org Release [1141 B]
+Get:14 http://incoming.debian.org Sources [16.2 kB]
+Get:15 http://incoming.debian.org Packages [140 kB]
+Get:16 http://ftp.de.debian.org unstable/contrib mips Packages [37.3 kB]
+Fetched 25.7 MB in 1min 11s (358 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,14 +72,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (895 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (709 kB/s)
Download complete and in download only mode
Check arch
@@ -102,58 +92,56 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-7)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -161,13 +149,12 @@ Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -177,165 +164,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 47 not upgraded.
-Need to get 17.2 MB of archives.
-After this operation, 49.5 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g mips 1:1.2.6.dfsg-2 [85.3 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 mips 5.9-4 [307 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.1-1 [36.7 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libssl1.0.0 mips 1.0.0h-1 [1089 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.10-1 [252 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.30.2-6 [1751 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-7 [859 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.4-2 [139 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libexpat1 mips 2.0.1-7.2 [143 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libdb4.8 mips 4.8.30-11 [661 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.1 [207 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.1-1 [1027 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.10-1 [52.8 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 mips 3.7.10-1 [454 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main python2.7-minimal mips 2.7.2-13 [1609 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main python2.7 mips 2.7.2-13 [2580 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-2 [28.6 kB]
-Get:32 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.6.dfsg-2 [211 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 44 not upgraded.
+Need to get 16.4 MB of archives.
+After this operation, 47.9 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libncursesw5 mips 5.9-10 [126 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.2-1 [37.1 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libssl1.0.0 mips 1.0.1c-4 [1121 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-9 [26.7 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.11-2 [201 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 1:8.31-1 [250 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libsqlite3-0 mips 3.7.14.1-1 [473 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-6 [869 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.33.12+really2.32.4-3 [1685 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.6-1 [118 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libexpat1 mips 2.1.0-1 [145 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-9 [139 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.3-1 [1032 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-9 [141 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main python2.7-minimal mips 2.7.3-5 [1615 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main python2.7 mips 2.7.3-5 [2605 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:27 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-9 [1918 kB]
+Get:28 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp.de.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
+Get:32 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.2 MB in 3s (5145 kB/s)
-(Reading database ... 10667 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_mips.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10667 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_mips.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mips.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mips.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_mips.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_mips.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mips.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mips.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mips.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mips.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mips.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mips.deb) ...
+Fetched 16.4 MB in 8s (2020 kB/s)
+Selecting previously unselected package libncursesw5:mips.
+(Reading database ... 10862 files and directories currently installed.)
+Unpacking libncursesw5:mips (from .../libncursesw5_5.9-10_mips.deb) ...
+Selecting previously unselected package libpipeline1:mips.
+Unpacking libpipeline1:mips (from .../libpipeline1_1.2.2-1_mips.deb) ...
+Selecting previously unselected package libssl1.0.0:mips.
+Unpacking libssl1.0.0:mips (from .../libssl1.0.0_1.0.1c-4_mips.deb) ...
+Selecting previously unselected package libasprintf0c2:mips.
+Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-9_mips.deb) ...
+Selecting previously unselected package libmagic1:mips.
+Unpacking libmagic1:mips (from .../libmagic1_5.11-2_mips.deb) ...
+Selecting previously unselected package libpcre3:mips.
+Unpacking libpcre3:mips (from .../libpcre3_1%3a8.31-1_mips.deb) ...
+Selecting previously unselected package libsqlite3-0:mips.
+Unpacking libsqlite3-0:mips (from .../libsqlite3-0_3.7.14.1-1_mips.deb) ...
+Selecting previously unselected package libxml2:mips.
+Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-6_mips.deb) ...
+Selecting previously unselected package libffi5:mips.
+Unpacking libffi5:mips (from .../libffi5_3.0.10-3_mips.deb) ...
+Selecting previously unselected package libglib2.0-0:mips.
+Unpacking libglib2.0-0:mips (from .../libglib2.0-0_2.33.12+really2.32.4-3_mips.deb) ...
+Selecting previously unselected package libcroco3:mips.
+Unpacking libcroco3:mips (from .../libcroco3_0.6.6-1_mips.deb) ...
+Selecting previously unselected package libexpat1:mips.
+Unpacking libexpat1:mips (from .../libexpat1_2.1.0-1_mips.deb) ...
+Selecting previously unselected package libunistring0:mips.
+Unpacking libunistring0:mips (from .../libunistring0_0.9.3-5_mips.deb) ...
+Selecting previously unselected package libgettextpo0:mips.
+Unpacking libgettextpo0:mips (from .../libgettextpo0_0.18.1.1-9_mips.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mips.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_mips.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_mips.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_mips.deb) ...
+Unpacking file (from .../archives/file_5.11-2_mips.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mips.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mips.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mips.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-13_mips.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_mips.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-13_mips.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_mips.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_mips.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_mips.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_mips.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_mips.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mips.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:mips.
+Unpacking zlib1g-dev:mips (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mips.deb) ...
+Setting up libncursesw5:mips (5.9-10) ...
+Setting up libpipeline1:mips (1.2.2-1) ...
+Setting up libssl1.0.0:mips (1.0.1c-4) ...
+Setting up libasprintf0c2:mips (0.18.1.1-9) ...
+Setting up libmagic1:mips (5.11-2) ...
+Setting up libpcre3:mips (1:8.31-1) ...
+Setting up libsqlite3-0:mips (3.7.14.1-1) ...
+Setting up libxml2:mips (2.8.0+dfsg1-6) ...
+Setting up libffi5:mips (3.0.10-3) ...
+Setting up libglib2.0-0:mips (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:mips (0.6.6-1) ...
+Setting up libexpat1:mips (2.1.0-1) ...
+Setting up libunistring0:mips (0.9.3-5) ...
+Setting up libgettextpo0:mips (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.2-13) ...
-Setting up python2.7 (2.7.2-13) ...
-Setting up python-minimal (2.7.2-10) ...
-Setting up python (2.7.2-10) ...
-Setting up cdbs (0.4.109) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:mips (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-0.bpo.1-octeon mips (mips64)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.4-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 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_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 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_3.10 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_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 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_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgomp1_4.6.2-12 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 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 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 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_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-13 python2.7-minimal_2.7.2-13 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mips (mips64)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -345,13 +330,13 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -362,18 +347,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture mips
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 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -389,11 +374,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -401,30 +386,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
-make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -435,7 +422,7 @@ CURRENT_VERSION = v2.16.1
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -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
@@ -510,7 +497,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -519,7 +506,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -569,10 +556,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -595,6 +585,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -638,7 +629,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -662,7 +653,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -676,6 +667,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -749,16 +741,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
cd debian/bedtools
- chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- cd '/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+ 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 '/build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0'
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
@@ -774,77 +788,85 @@ dh_fixperms -pbedtools
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 /build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-mips-IQCOA2/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
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
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../bedtools_2.16.1-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_mips.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../bedtools_2.17.0-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1256
+Build finished at 20121104-1156
-bedtools_2.16.1-1_mips.changes:
+bedtools_2.17.0-1_mips.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
+Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 294633473dfee43e31f80c55eba2198c8f9b1d2d 354186 bedtools_2.16.1-1_mips.deb
+ 67ca843836063970cba2c984f9ad08bd52c1abf0 371766 bedtools_2.17.0-1_mips.deb
Checksums-Sha256:
- 0f319d419654b948cc905235c6becc025d3a75c194026367adfb0860c3423234 354186 bedtools_2.16.1-1_mips.deb
+ 1eae5c9e021309048a7a40bc1a1177549f0a79a35e2bc12549d23a23aaa7981f 371766 bedtools_2.17.0-1_mips.deb
Files:
- ead6be44f11d8c16cf85f0503f773e94 354186 science optional bedtools_2.16.1-1_mips.deb
+ 2f469fdf8a63130641e56b1bca9e425d 371766 science optional bedtools_2.17.0-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_mips.deb
+bedtools_2.17.0-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 354186 bytes: control archive= 1981 bytes.
- 864 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 371766 bytes: control archive= 4114 bytes.
+ 32 bytes, 1 lines conffiles
+ 832 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1503
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1673
+ Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -858,58 +880,168 @@ bedtools_2.16.1-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:17 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/annotateBed
--rwxr-xr-x root/root 1477568 2012-03-16 12:55 ./usr/bin/bedtools
--rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/nucBed
--rwxr-xr-x root/root 36 2012-03-16 12:55 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/coverageBed
--rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/tagBam
--rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/flankBed
--rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/mergeBed
--rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/mapBed
--rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/pairToPair
--rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/randomBed
--rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/bamToBed
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/subtractBed
--rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/clusterBed
--rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/getOverlap
--rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 36 2012-03-16 12:55 ./usr/bin/windowMaker
--rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/pairToBed
--rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/expandCols
--rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/windowBed
--rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/intersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/bedToBam
--rwxr-xr-x root/root 29 2012-03-16 12:55 ./usr/bin/slopBed
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 29 2012-03-16 12:55 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/closestBed
--rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/bedToIgv
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./usr/bin/
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 39 2012-11-04 11:55 ./usr/bin/randomBed
+-rwxr-xr-x root/root 44 2012-11-04 11:55 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 44 2012-11-04 11:55 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 38 2012-11-04 11:55 ./usr/bin/linksBed
+-rwxr-xr-x root/root 36 2012-11-04 11:55 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 36 2012-11-04 11:55 ./usr/bin/tagBam
+-rwxr-xr-x root/root 43 2012-11-04 11:55 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 40 2012-11-04 11:55 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 40 2012-11-04 11:55 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 42 2012-11-04 11:55 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:55 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 37 2012-11-04 11:55 ./usr/bin/sortBed
+-rwxr-xr-x root/root 42 2012-11-04 11:55 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 42 2012-11-04 11:55 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 43 2012-11-04 11:55 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 43 2012-11-04 11:55 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 36 2012-11-04 11:55 ./usr/bin/nucBed
+-rwxr-xr-x root/root 1506976 2012-11-04 11:55 ./usr/bin/bedtools
+-rwxr-xr-x root/root 40 2012-11-04 11:55 ./usr/bin/closestBed
+-rwxr-xr-x root/root 39 2012-11-04 11:55 ./usr/bin/windowBed
+-rwxr-xr-x root/root 38 2012-11-04 11:55 ./usr/bin/flankBed
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:55 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 42 2012-11-04 11:55 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 40 2012-11-04 11:55 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 11:55 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 37 2012-11-04 11:55 ./usr/bin/slopBed
+-rwxr-xr-x root/root 39 2012-11-04 11:55 ./usr/bin/expandCols
+-rwxr-xr-x root/root 36 2012-11-04 11:55 ./usr/bin/mapBed
+-rwxr-xr-x root/root 42 2012-11-04 11:55 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:55 ./usr/bin/complementBed
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:55 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -923,33 +1055,31 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-badc569c-02d4-48df-8386-c5135e2e7775/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl
+Purging /var/lib/schroot/mount/sid-mips-sbuild-68550864-1670-492e-8259-3667f3102a25/build/buildd-bedtools_2.17.0-1-mips-IQCOA2
Not cleaning session: cloned chroot in use
-Can't open average time db /var/lib/sbuild/avg-build-times
-Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 78100
-Build-Time: 2348
+Build-Space: 80832
+Build-Time: 1385
Distribution: sid
-Install-Time: 112
-Job: bedtools_2.16.1-1
+Install-Time: 150
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 2605
-Source-Version: 2.16.1-1
-Space: 78100
+Package-Time: 1667
+Source-Version: 2.17.0-1
+Space: 80832
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1256
-Build needed 00:43:25, 78100k disc space
-Signature with key 'B5319330' requested:
+Finished at 20121104-1156
+Build needed 00:27:47, 80832k disc space
+Signature with key 'E348DA45' requested:
-From buildd at mayer.debian.org Fri Mar 16 12:41:35 2012
+From buildd at mayer.debian.org Sun Nov 04 11:55:06 2012
Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -957,23 +1087,23 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1S8WTO-0008SW-KI
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:34 +0000
+ id 1TUynB-0004MB-S4
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:06 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1S8WTM-0006kt-Sj
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:33 +0000
+ id 1TUyn9-0006lO-Sk
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:04 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1S8WTJ-0000nS-NG
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:29 +0000
-Date: Fri, 16 Mar 2012 12:41:29 +0000
-Message-Id: <E1S8WTJ-0000nS-NG at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1TUyn6-0006rb-Eo
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:00 +0000
+Date: Sun, 04 Nov 2012 11:55:00 +0000
+Message-Id: <E1TUyn6-0006rb-Eo at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.17.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -981,146 +1111,29 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (mipsel) 16 Mar 2012 12:15 ║
+║ bedtools 2.17.0-1 (mipsel) 04 Nov 2012 11:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: mipsel
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Hit http://debian.oregonstate.edu sid InRelease
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
Get:1 http://incoming.debian.org Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release [1616 B]
+Get:2 http://incoming.debian.org Release [1141 B]
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Hit http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://debian.oregonstate.edu sid/main Translation-en
Hit http://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:3 http://incoming.debian.org Sources [58.9 kB]
-Get:4 http://incoming.debian.org Packages [687 kB]
-Hit http://incoming.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 748 kB in 5s (127 kB/s)
+Get:3 http://incoming.debian.org Sources [16.2 kB]
+Get:4 http://incoming.debian.org Packages [140 kB]
+Fetched 158 kB in 2s (75.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1132,92 +1145,20 @@ Check APT
─────────
Checking available source versions...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Download source files with APT
──────────────────────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 2s (375 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (791 kB/s)
Download complete and in download only mode
Check arch
@@ -1230,549 +1171,196 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Installing positive dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Removing negative dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-27)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1 libpipeline1
- libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
- po-debconf python-minimal python2.7 python2.7-minimal
+ libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
python-doc python-tk python2.7-doc binfmt-support procmail graphviz
default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
- mime-support po-debconf python python-minimal python2.7 python2.7-minimal
- quilt zlib1g-dev
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 29 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0 B/16.3 MB of archives.
-After this operation, 47.9 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1.
-(Reading database ... 11081 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mipsel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_mipsel.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_mipsel.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mipsel.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mipsel.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mipsel.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mipsel.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mipsel.deb) ...
+0 upgraded, 31 newly installed, 0 to remove and 22 not upgraded.
+Need to get 0 B/15.8 MB of archives.
+After this operation, 46.8 MB of additional disk space will be used.
+Selecting previously unselected package libncursesw5:mipsel.
+(Reading database ... 10941 files and directories currently installed.)
+Unpacking libncursesw5:mipsel (from .../libncursesw5_5.9-10_mipsel.deb) ...
+Selecting previously unselected package libpipeline1:mipsel.
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+Selecting previously unselected package libssl1.0.0:mipsel.
+Unpacking libssl1.0.0:mipsel (from .../libssl1.0.0_1.0.1c-4_mipsel.deb) ...
+Selecting previously unselected package libasprintf0c2:mipsel.
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Selecting previously unselected package libmagic1:mipsel.
+Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Selecting previously unselected package libsqlite3-0:mipsel.
+Unpacking libsqlite3-0:mipsel (from .../libsqlite3-0_3.7.14.1-1_mipsel.deb) ...
+Selecting previously unselected package libxml2:mipsel.
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-6_mipsel.deb) ...
+Selecting previously unselected package libffi5:mipsel.
+Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
+Selecting previously unselected package libglib2.0-0:mipsel.
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-3_mipsel.deb) ...
+Selecting previously unselected package libcroco3:mipsel.
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-1_mipsel.deb) ...
+Selecting previously unselected package libexpat1:mipsel.
+Unpacking libexpat1:mipsel (from .../libexpat1_2.1.0-1_mipsel.deb) ...
+Selecting previously unselected package libunistring0:mipsel.
+Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package libgettextpo0:mipsel.
+Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_mipsel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.10-1_mipsel.deb) ...
+Unpacking file (from .../file_5.11-2_mipsel.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_mipsel.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_mipsel.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_mipsel.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_mipsel.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mipsel.deb) ...
-Setting up libpipeline1 (1.2.1-1) ...
-Setting up libssl1.0.0 (1.0.0h-1) ...
-Setting up libmagic1 (5.10-1) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:mipsel.
+Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
+Setting up libncursesw5:mipsel (5.9-10) ...
+Setting up libpipeline1:mipsel (1.2.2-1) ...
+Setting up libssl1.0.0:mipsel (1.0.1c-4) ...
+Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
+Setting up libmagic1:mipsel (5.11-2) ...
+Setting up libsqlite3-0:mipsel (3.7.14.1-1) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-6) ...
+Setting up libffi5:mipsel (3.0.10-3) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 (2.6.1-1) ...
+Setting up libcroco3:mipsel (0.6.6-1) ...
+Setting up libexpat1:mipsel (2.1.0-1) ...
+Setting up libunistring0:mipsel (0.9.3-5) ...
+Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:mipsel (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-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_3.2.4-1
-Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 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-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 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_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 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_2.20.1-3 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 libdevmapper1.02.1_2:1.02.67-2 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 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-3 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 libprocps0_1:3.3.2-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42-1 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 libudev0_175-3.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 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 procps_1:3.3.2-3 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 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 udev_175-3.1 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-35 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.5 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1782,49 +1370,13 @@ Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 bin
Unpack source
─────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1834,55 +1386,19 @@ Check disc space
dpkg-buildpackage
─────────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture mipsel
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 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -1898,11 +1414,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1910,30 +1426,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -1944,7 +1462,7 @@ CURRENT_VERSION = v2.16.1
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -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
@@ -2019,7 +1537,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -2028,7 +1546,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -2078,10 +1596,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -2104,6 +1625,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -2147,7 +1669,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -2171,7 +1693,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -2185,6 +1707,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -2258,16 +1781,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
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
@@ -2283,38 +1828,42 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
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
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.16.1-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.17.0-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1240
+Build finished at 20121104-1154
-bedtools_2.16.1-1_mipsel.changes:
+bedtools_2.17.0-1_mipsel.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -2322,38 +1871,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- d44fe88544215759e97f1f0e02912cb1dd650530 363526 bedtools_2.16.1-1_mipsel.deb
+ 5382b9047b1e8b599dd2f3b3c19ddfbfb9a69f53 380730 bedtools_2.17.0-1_mipsel.deb
Checksums-Sha256:
- 77de6839d9d0bca335452cbcb333518502bd5aad221da61ce914821d075ddd7b 363526 bedtools_2.16.1-1_mipsel.deb
+ fd2f0467716f7b441625457b79004062282bc9823e989bf42da7349d969cad4d 380730 bedtools_2.17.0-1_mipsel.deb
Files:
- 6fe24a0483cfa020297c9334647f3b95 363526 science optional bedtools_2.16.1-1_mipsel.deb
+ 7b9993857e35e2722c06d686b487a0d0 380730 science optional bedtools_2.17.0-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_mipsel.deb
+bedtools_2.17.0-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 363526 bytes: control archive= 1978 bytes.
- 866 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 380730 bytes: control archive= 4110 bytes.
+ 32 bytes, 1 lines conffiles
+ 834 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1503
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1673
+ Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -2367,58 +1920,168 @@ bedtools_2.16.1-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bedToBam
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 1477568 2012-03-16 12:40 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/coverageBed
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/flankBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/intersectBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/mapBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/pairToBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/pairToPair
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/slopBed
--rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/tagBam
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
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+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
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+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-abce8984-ccea-45e3-a5dc-d4e7d91e4372/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo
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+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Reading package lists...
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The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libdb4.8* libexpat1* libffi5*
- libglib2.0-0* libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0*
- libunistring0* libxml2* man-db* mime-support* po-debconf* python*
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+ html2text* intltool-debian* libasprintf0c2* libcroco3* libexpat1* libffi5*
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+ libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db* mime-support*
+ po-debconf* python* python-minimal* python2.7* python2.7-minimal* quilt*
+ zlib1g-dev*
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Purging configuration files for groff-base ...
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+Removing libcroco3:mipsel ...
+Purging configuration files for libcroco3:mipsel ...
Removing python ...
Purging configuration files for python ...
Removing python2.7 ...
Purging configuration files for python2.7 ...
-Removing libdb4.8 ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libsqlite3-0 ...
-Purging configuration files for libsqlite3-0 ...
+Removing libexpat1:mipsel ...
+Purging configuration files for libexpat1:mipsel ...
+Removing libglib2.0-0:mipsel ...
+Purging configuration files for libglib2.0-0:mipsel ...
+Removing libffi5:mipsel ...
+Purging configuration files for libffi5:mipsel ...
+Removing libgettextpo0:mipsel ...
+Removing libmagic1:mipsel ...
+Purging configuration files for libmagic1:mipsel ...
+Removing libncursesw5:mipsel ...
+Purging configuration files for libncursesw5:mipsel ...
+Removing libpipeline1:mipsel ...
+Purging configuration files for libpipeline1:mipsel ...
+Removing libsqlite3-0:mipsel ...
+Purging configuration files for libsqlite3-0:mipsel ...
+Removing libssl1.0.0:mipsel ...
+Purging configuration files for libssl1.0.0:mipsel ...
+Removing libunistring0:mipsel ...
+Purging configuration files for libunistring0:mipsel ...
+Removing libxml2:mipsel ...
+Purging configuration files for libxml2:mipsel ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
Removing python-minimal ...
Removing python2.7-minimal ...
Purging configuration files for python2.7-minimal ...
-Removing libssl1.0.0 ...
-Purging configuration files for libssl1.0.0 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing mime-support ...
-Purging configuration files for mime-support ...
-Removing zlib1g-dev ...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
+Removing zlib1g-dev:mipsel ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 78100
-Build-Time: 1338
+Build-Space: 80836
+Build-Time: 1442
Distribution: sid
-Install-Time: 108
-Job: bedtools_2.16.1-1
+Install-Time: 79
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 1536
-Source-Version: 2.16.1-1
-Space: 78100
+Package-Time: 1578
+Source-Version: 2.17.0-1
+Space: 80836
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1240
-Build needed 00:25:36, 78100k disc space
+Finished at 20121104-1154
+Build needed 00:26:18, 80836k disc space
Signature with key '8C9FAB20' requested:
diff --git a/mipsel.log b/mipsel.log
index 45d687d..e7632bf 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,4 +1,4 @@
-From buildd at mayer.debian.org Fri Mar 16 12:41:35 2012
+From buildd at mayer.debian.org Sun Nov 04 11:55:06 2012
Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,23 +6,23 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1S8WTO-0008SW-KI
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:34 +0000
+ id 1TUynB-0004MB-S4
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:06 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1S8WTM-0006kt-Sj
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:33 +0000
+ id 1TUyn9-0006lO-Sk
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:04 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1S8WTJ-0000nS-NG
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:29 +0000
-Date: Fri, 16 Mar 2012 12:41:29 +0000
-Message-Id: <E1S8WTJ-0000nS-NG at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1TUyn6-0006rb-Eo
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:55:00 +0000
+Date: Sun, 04 Nov 2012 11:55:00 +0000
+Message-Id: <E1TUyn6-0006rb-Eo at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.17.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,146 +30,29 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (mipsel) 16 Mar 2012 12:15 ║
+║ bedtools 2.17.0-1 (mipsel) 04 Nov 2012 11:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: mipsel
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Hit http://debian.oregonstate.edu sid InRelease
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
Get:1 http://incoming.debian.org Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release [1616 B]
+Get:2 http://incoming.debian.org Release [1141 B]
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Hit http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://debian.oregonstate.edu sid/main Translation-en
Hit http://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:3 http://incoming.debian.org Sources [58.9 kB]
-Get:4 http://incoming.debian.org Packages [687 kB]
-Hit http://incoming.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 748 kB in 5s (127 kB/s)
+Get:3 http://incoming.debian.org Sources [16.2 kB]
+Get:4 http://incoming.debian.org Packages [140 kB]
+Fetched 158 kB in 2s (75.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -181,92 +64,20 @@ Check APT
─────────
Checking available source versions...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Download source files with APT
──────────────────────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 2s (375 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (791 kB/s)
Download complete and in download only mode
Check arch
@@ -279,549 +90,196 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Installing positive dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Removing negative dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-14)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-27)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1 libpipeline1
- libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
- po-debconf python-minimal python2.7 python2.7-minimal
+ libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
python-doc python-tk python2.7-doc binfmt-support procmail graphviz
default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
- mime-support po-debconf python python-minimal python2.7 python2.7-minimal
- quilt zlib1g-dev
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 29 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0 B/16.3 MB of archives.
-After this operation, 47.9 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1.
-(Reading database ... 11081 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mipsel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_mipsel.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_mipsel.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mipsel.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mipsel.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mipsel.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mipsel.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mipsel.deb) ...
+0 upgraded, 31 newly installed, 0 to remove and 22 not upgraded.
+Need to get 0 B/15.8 MB of archives.
+After this operation, 46.8 MB of additional disk space will be used.
+Selecting previously unselected package libncursesw5:mipsel.
+(Reading database ... 10941 files and directories currently installed.)
+Unpacking libncursesw5:mipsel (from .../libncursesw5_5.9-10_mipsel.deb) ...
+Selecting previously unselected package libpipeline1:mipsel.
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+Selecting previously unselected package libssl1.0.0:mipsel.
+Unpacking libssl1.0.0:mipsel (from .../libssl1.0.0_1.0.1c-4_mipsel.deb) ...
+Selecting previously unselected package libasprintf0c2:mipsel.
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Selecting previously unselected package libmagic1:mipsel.
+Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Selecting previously unselected package libsqlite3-0:mipsel.
+Unpacking libsqlite3-0:mipsel (from .../libsqlite3-0_3.7.14.1-1_mipsel.deb) ...
+Selecting previously unselected package libxml2:mipsel.
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-6_mipsel.deb) ...
+Selecting previously unselected package libffi5:mipsel.
+Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
+Selecting previously unselected package libglib2.0-0:mipsel.
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-3_mipsel.deb) ...
+Selecting previously unselected package libcroco3:mipsel.
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-1_mipsel.deb) ...
+Selecting previously unselected package libexpat1:mipsel.
+Unpacking libexpat1:mipsel (from .../libexpat1_2.1.0-1_mipsel.deb) ...
+Selecting previously unselected package libunistring0:mipsel.
+Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package libgettextpo0:mipsel.
+Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_mipsel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.10-1_mipsel.deb) ...
+Unpacking file (from .../file_5.11-2_mipsel.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_mipsel.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_mipsel.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_mipsel.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_mipsel.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mipsel.deb) ...
-Setting up libpipeline1 (1.2.1-1) ...
-Setting up libssl1.0.0 (1.0.0h-1) ...
-Setting up libmagic1 (5.10-1) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:mipsel.
+Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
+Setting up libncursesw5:mipsel (5.9-10) ...
+Setting up libpipeline1:mipsel (1.2.2-1) ...
+Setting up libssl1.0.0:mipsel (1.0.1c-4) ...
+Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
+Setting up libmagic1:mipsel (5.11-2) ...
+Setting up libsqlite3-0:mipsel (3.7.14.1-1) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-6) ...
+Setting up libffi5:mipsel (3.0.10-3) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 (2.6.1-1) ...
+Setting up libcroco3:mipsel (0.6.6-1) ...
+Setting up libexpat1:mipsel (2.1.0-1) ...
+Setting up libunistring0:mipsel (0.9.3-5) ...
+Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:mipsel (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-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_3.2.4-1
-Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 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-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 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_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 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_2.20.1-3 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 libdevmapper1.02.1_2:1.02.67-2 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 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-3 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 libprocps0_1:3.3.2-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42-1 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 libudev0_175-3.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 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 procps_1:3.3.2-3 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 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 udev_175-3.1 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-35 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.5 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-14 perl-base_5.14.2-14 perl-modules_5.14.2-14 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012g-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -831,49 +289,13 @@ Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 bin
Unpack source
─────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -883,55 +305,19 @@ Check disc space
dpkg-buildpackage
─────────────────
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture mipsel
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 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -947,11 +333,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -959,30 +345,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -993,7 +381,7 @@ CURRENT_VERSION = v2.16.1
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -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
@@ -1068,7 +456,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -1077,7 +465,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -1127,10 +515,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -1153,6 +544,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -1196,7 +588,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -1220,7 +612,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -1234,6 +626,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -1307,16 +700,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0'
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
@@ -1332,38 +747,42 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
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
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.16.1-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.17.0-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1240
+Build finished at 20121104-1154
-bedtools_2.16.1-1_mipsel.changes:
+bedtools_2.17.0-1_mipsel.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -1371,38 +790,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- d44fe88544215759e97f1f0e02912cb1dd650530 363526 bedtools_2.16.1-1_mipsel.deb
+ 5382b9047b1e8b599dd2f3b3c19ddfbfb9a69f53 380730 bedtools_2.17.0-1_mipsel.deb
Checksums-Sha256:
- 77de6839d9d0bca335452cbcb333518502bd5aad221da61ce914821d075ddd7b 363526 bedtools_2.16.1-1_mipsel.deb
+ fd2f0467716f7b441625457b79004062282bc9823e989bf42da7349d969cad4d 380730 bedtools_2.17.0-1_mipsel.deb
Files:
- 6fe24a0483cfa020297c9334647f3b95 363526 science optional bedtools_2.16.1-1_mipsel.deb
+ 7b9993857e35e2722c06d686b487a0d0 380730 science optional bedtools_2.17.0-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_mipsel.deb
+bedtools_2.17.0-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 363526 bytes: control archive= 1978 bytes.
- 866 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 380730 bytes: control archive= 4110 bytes.
+ 32 bytes, 1 lines conffiles
+ 834 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1503
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1673
+ Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -1416,58 +839,168 @@ bedtools_2.16.1-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bedToBam
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 1477568 2012-03-16 12:40 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/closestBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/clusterBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/complementBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/coverageBed
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/expandCols
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/flankBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/intersectBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/linksBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/mapBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/nucBed
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/pairToBed
--rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/pairToPair
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/slopBed
--rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/sortBed
--rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/subtractBed
--rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/tagBam
--rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/windowBed
--rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/windowMaker
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:53 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:30 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
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+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-abce8984-ccea-45e3-a5dc-d4e7d91e4372/build/buildd-bedtools_2.17.0-1-mipsel-ZcMMwo
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Reading package lists...
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The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libdb4.8* libexpat1* libffi5*
- libglib2.0-0* libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0*
- libunistring0* libxml2* man-db* mime-support* po-debconf* python*
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+ po-debconf* python* python-minimal* python2.7* python2.7-minimal* quilt*
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-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
+Removing zlib1g-dev:mipsel ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 78100
-Build-Time: 1338
+Build-Space: 80836
+Build-Time: 1442
Distribution: sid
-Install-Time: 108
-Job: bedtools_2.16.1-1
+Install-Time: 79
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 1536
-Source-Version: 2.16.1-1
-Space: 78100
+Package-Time: 1578
+Source-Version: 2.17.0-1
+Space: 80836
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1240
-Build needed 00:25:36, 78100k disc space
+Finished at 20121104-1154
+Build needed 00:26:18, 80836k disc space
Signature with key '8C9FAB20' requested:
diff --git a/powerpc.log b/powerpc.log
index 343b10c..badfdcd 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,70 +1,59 @@
-From buildd at praetorius.debian.org Fri Mar 16 14:20:07 2012
-Return-path: <buildd at praetorius.debian.org>
+From buildd at parry.debian.org Sun Nov 04 11:35:37 2012
+Return-path: <buildd at parry.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1S8Y0l-0004KR-J7
- for logs at buildd.debian.org; Fri, 16 Mar 2012 14:20:07 +0000
-Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
- (helo=praetorius.debian.org)
+ (Exim 4.72) (envelope-from <buildd at parry.debian.org>)
+ id 1TUyUK-0001Em-Lv
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:35:36 +0000
+Received: from parry.debian.org ([140.211.15.153])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=praetorius.debian.org,
- EMAIL=hostmaster at praetorius.debian.org (verified)
+ CN=parry.debian.org, EMAIL=hostmaster at parry.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1S8Y0k-0005jF-Gs; Fri, 16 Mar 2012 14:20:06 +0000
-Received: from buildd by praetorius.debian.org with local (Exim 4.72)
- (envelope-from <buildd at praetorius.debian.org>)
- id 1S8Y0j-0004Ad-FV; Fri, 16 Mar 2012 14:20:05 +0000
-Date: Fri, 16 Mar 2012 14:20:05 +0000
-Message-Id: <E1S8Y0j-0004Ad-FV at praetorius.debian.org>
-From: buildd on praetorius <buildd at praetorius.debian.org>
-To: wouter at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on powerpc (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at parry.debian.org>)
+ id 1TUyUI-000548-WF; Sun, 04 Nov 2012 11:35:35 +0000
+Received: from buildd by parry.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at parry.debian.org>)
+ id 1TUyUG-0002rv-6a; Sun, 04 Nov 2012 11:35:32 +0000
+Date: Sun, 04 Nov 2012 11:35:32 +0000
+Message-Id: <E1TUyUG-0002rv-6a at parry.debian.org>
+From: buildd on parry <buildd at parry.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on powerpc (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on parry.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (powerpc) 16 Mar 2012 14:13 ║
+║ bedtools 2.17.0-1 (powerpc) 04 Nov 2012 11:31 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: powerpc
-Get:1 http://ftp.se.debian.org unstable InRelease [198 kB]
-Get:2 http://ftp.se.debian.org unstable/main Sources [6213 kB]
-Get:3 http://incoming.debian.org unstable InRelease [198 kB]
-Get:4 http://ftp.se.debian.org unstable/contrib Sources [54.4 kB]
-Get:5 http://ftp.se.debian.org unstable/non-free Sources [99.8 kB]
-Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [5823 kB]
-Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [37.1 kB]
-Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2223 B]
-Get:9 http://ftp.se.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:10 http://ftp.se.debian.org unstable/main Translation-en [3902 kB]
+Get:1 http://incoming.debian.org unstable InRelease [219 kB]
+Get:2 http://debian.osuosl.org unstable InRelease [219 kB]
+Get:3 http://debian.osuosl.org unstable/main Sources [6381 kB]
+Get:4 http://debian.osuosl.org unstable/contrib Sources [53.1 kB]
+Get:5 http://debian.osuosl.org unstable/non-free Sources [101 kB]
+Get:6 http://debian.osuosl.org unstable/main powerpc Packages [6074 kB]
Ign http://incoming.debian.org InRelease
-Get:11 http://incoming.debian.org Release.gpg [836 B]
-Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main powerpc Packages [5823 kB]
-Get:16 http://incoming.debian.org unstable/contrib powerpc Packages [37.1 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [62.0 kB]
-Get:22 http://incoming.debian.org Packages [695 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.5 MB in 19s (1730 kB/s)
+Get:7 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:8 http://debian.osuosl.org unstable/contrib powerpc Packages [37.0 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main powerpc Packages [6074 kB]
+Get:12 http://incoming.debian.org unstable/contrib powerpc Packages [37.0 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.9 MB in 9s (2876 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,12 +73,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (530 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (926 kB/s)
Download complete and in download only mode
Check arch
@@ -103,58 +92,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.10)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-13)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-24)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.2)
+mount: already installed (2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -165,10 +154,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python-minimal
+ python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -178,165 +167,158 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 61 not upgraded.
-Need to get 17.6 MB of archives.
-After this operation, 48.9 MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org/debian/ unstable/main zlib1g powerpc 1:1.2.6.dfsg-2 [84.9 kB]
-Get:2 http://ftp.se.debian.org/debian/ unstable/main libncursesw5 powerpc 5.9-4 [314 kB]
-Get:3 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
-Get:4 http://ftp.se.debian.org/debian/ unstable/main libssl1.0.0 powerpc 1.0.0h-1 [1133 kB]
-Get:5 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.10-1 [255 kB]
-Get:6 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:7 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
-Get:8 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.30.2-6 [1800 kB]
-Get:9 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-7 [842 kB]
-Get:10 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.4-2 [142 kB]
-Get:11 http://ftp.se.debian.org/debian/ unstable/main libexpat1 powerpc 2.0.1-7.2 [138 kB]
-Get:12 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:13 http://ftp.se.debian.org/debian/ unstable/main libdb4.8 powerpc 4.8.30-11 [694 kB]
-Get:14 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.1 [208 kB]
-Get:15 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:16 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.1-1 [1055 kB]
-Get:17 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.10-1 [52.9 kB]
-Get:18 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
-Get:19 http://ftp.se.debian.org/debian/ unstable/main libsqlite3-0 powerpc 3.7.10-1 [431 kB]
-Get:20 http://ftp.se.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://ftp.se.debian.org/debian/ unstable/main python2.7-minimal powerpc 2.7.3~rc1-1 [1748 kB]
-Get:22 http://ftp.se.debian.org/debian/ unstable/main python2.7 powerpc 2.7.3~rc1-1 [2618 kB]
-Get:23 http://ftp.se.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://ftp.se.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:26 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:27 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
-Get:28 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:29 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://ftp.se.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-2 [29.1 kB]
-Get:32 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.6.dfsg-2 [209 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python
+ python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 30 not upgraded.
+Need to get 16.4 MB of archives.
+After this operation, 46.9 MB of additional disk space will be used.
+Get:1 http://debian.osuosl.org/debian/ unstable/main libncursesw5 powerpc 5.9-10 [132 kB]
+Get:2 http://debian.osuosl.org/debian/ unstable/main libpipeline1 powerpc 1.2.2-1 [39.0 kB]
+Get:3 http://debian.osuosl.org/debian/ unstable/main libssl1.0.0 powerpc 1.0.1c-4 [1178 kB]
+Get:4 http://debian.osuosl.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-9 [27.0 kB]
+Get:5 http://debian.osuosl.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
+Get:6 http://debian.osuosl.org/debian/ unstable/main libsqlite3-0 powerpc 3.7.14.1-1 [451 kB]
+Get:7 http://debian.osuosl.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-6 [851 kB]
+Get:8 http://debian.osuosl.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:9 http://debian.osuosl.org/debian/ unstable/main libglib2.0-0 powerpc 2.33.12+really2.32.4-3 [1713 kB]
+Get:10 http://debian.osuosl.org/debian/ unstable/main libcroco3 powerpc 0.6.6-1 [121 kB]
+Get:11 http://debian.osuosl.org/debian/ unstable/main libexpat1 powerpc 2.1.0-1 [142 kB]
+Get:12 http://debian.osuosl.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:13 http://debian.osuosl.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-9 [137 kB]
+Get:14 http://debian.osuosl.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
+Get:15 http://debian.osuosl.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
+Get:16 http://debian.osuosl.org/debian/ unstable/main man-db powerpc 2.6.3-1 [1051 kB]
+Get:17 http://debian.osuosl.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
+Get:18 http://debian.osuosl.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-9 [131 kB]
+Get:19 http://debian.osuosl.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:20 http://debian.osuosl.org/debian/ unstable/main python2.7-minimal powerpc 2.7.3-5 [1753 kB]
+Get:21 http://debian.osuosl.org/debian/ unstable/main python2.7 powerpc 2.7.3-5 [2644 kB]
+Get:22 http://debian.osuosl.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:23 http://debian.osuosl.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:24 http://debian.osuosl.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:25 http://debian.osuosl.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:26 http://debian.osuosl.org/debian/ unstable/main gettext powerpc 0.18.1.1-9 [1929 kB]
+Get:27 http://debian.osuosl.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://debian.osuosl.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://debian.osuosl.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:30 http://debian.osuosl.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
+Get:31 http://debian.osuosl.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:32 http://debian.osuosl.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.6 MB in 1s (9565 kB/s)
-(Reading database ... 10672 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_powerpc.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10672 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_powerpc.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_powerpc.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_powerpc.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_powerpc.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_powerpc.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_powerpc.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_powerpc.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_powerpc.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_powerpc.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_powerpc.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_powerpc.deb) ...
+Fetched 16.4 MB in 2s (7075 kB/s)
+Selecting previously unselected package libncursesw5:powerpc.
+(Reading database ... 10923 files and directories currently installed.)
+Unpacking libncursesw5:powerpc (from .../libncursesw5_5.9-10_powerpc.deb) ...
+Selecting previously unselected package libpipeline1:powerpc.
+Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.2-1_powerpc.deb) ...
+Selecting previously unselected package libssl1.0.0:powerpc.
+Unpacking libssl1.0.0:powerpc (from .../libssl1.0.0_1.0.1c-4_powerpc.deb) ...
+Selecting previously unselected package libasprintf0c2:powerpc.
+Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-9_powerpc.deb) ...
+Selecting previously unselected package libmagic1:powerpc.
+Unpacking libmagic1:powerpc (from .../libmagic1_5.11-2_powerpc.deb) ...
+Selecting previously unselected package libsqlite3-0:powerpc.
+Unpacking libsqlite3-0:powerpc (from .../libsqlite3-0_3.7.14.1-1_powerpc.deb) ...
+Selecting previously unselected package libxml2:powerpc.
+Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-6_powerpc.deb) ...
+Selecting previously unselected package libffi5:powerpc.
+Unpacking libffi5:powerpc (from .../libffi5_3.0.10-3_powerpc.deb) ...
+Selecting previously unselected package libglib2.0-0:powerpc.
+Unpacking libglib2.0-0:powerpc (from .../libglib2.0-0_2.33.12+really2.32.4-3_powerpc.deb) ...
+Selecting previously unselected package libcroco3:powerpc.
+Unpacking libcroco3:powerpc (from .../libcroco3_0.6.6-1_powerpc.deb) ...
+Selecting previously unselected package libexpat1:powerpc.
+Unpacking libexpat1:powerpc (from .../libexpat1_2.1.0-1_powerpc.deb) ...
+Selecting previously unselected package libunistring0:powerpc.
+Unpacking libunistring0:powerpc (from .../libunistring0_0.9.3-5_powerpc.deb) ...
+Selecting previously unselected package libgettextpo0:powerpc.
+Unpacking libgettextpo0:powerpc (from .../libgettextpo0_0.18.1.1-9_powerpc.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_powerpc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_powerpc.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_powerpc.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_powerpc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.10-1_powerpc.deb) ...
+Unpacking file (from .../file_5.11-2_powerpc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_powerpc.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_powerpc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_powerpc.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_powerpc.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_powerpc.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_powerpc.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_powerpc.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_powerpc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_powerpc.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_powerpc.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_powerpc.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_powerpc.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:powerpc.
+Unpacking zlib1g-dev:powerpc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_powerpc.deb) ...
+Setting up libncursesw5:powerpc (5.9-10) ...
+Setting up libpipeline1:powerpc (1.2.2-1) ...
+Setting up libssl1.0.0:powerpc (1.0.1c-4) ...
+Setting up libasprintf0c2:powerpc (0.18.1.1-9) ...
+Setting up libmagic1:powerpc (5.11-2) ...
+Setting up libsqlite3-0:powerpc (3.7.14.1-1) ...
+Setting up libxml2:powerpc (2.8.0+dfsg1-6) ...
+Setting up libffi5:powerpc (3.0.10-3) ...
+Setting up libglib2.0-0:powerpc (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:powerpc (0.6.6-1) ...
+Setting up libexpat1:powerpc (2.1.0-1) ...
+Setting up libunistring0:powerpc (0.9.3-5) ...
+Setting up libgettextpo0:powerpc (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:powerpc (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 61 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.22-3 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_3.2.1-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 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_9.20120312 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_5.10-1 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-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-10 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_3.10 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_2.20.1-1.2 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_0.6.4-2 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_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 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_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 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_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2.1 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-10 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-3 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-10 gcc-4.6_4.6.3-10 libc6-dev_2.13-35 libstdc++6_4.7.2-2 libstdc++6-4.6-dev_4.6.3-10 linux-libc-dev_3.2.30-1
+Package versions: apt_0.9.7.5 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-10 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-10 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-10 gcc-4.6-base_4.6.3-10 gcc-4.7-base_4.7.2-2 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.5 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-2 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-2 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-2 libstdc++6-4.6-dev_4.6.3-10 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.30-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.2 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-13 perl-base_5.14.2-13 perl-modules_5.14.2-13 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012f-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -347,12 +329,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -363,18 +345,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture powerpc
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -390,11 +372,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -402,30 +384,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -436,7 +420,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -511,7 +495,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -520,7 +504,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -570,10 +554,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -596,6 +583,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -639,7 +627,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -663,7 +651,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -677,6 +665,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -750,16 +739,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0'
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
@@ -775,8 +786,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -786,66 +800,70 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.16.1-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (parry) <buildd_powerpc-parry at buildd.debian.org> >../bedtools_2.17.0-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1420
+Build finished at 20121104-1135
-bedtools_2.16.1-1_powerpc.changes:
+bedtools_2.17.0-1_powerpc.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
+Maintainer: powerpc Build Daemon (parry) <buildd_powerpc-parry at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 56935389cf63de0f257ae01c49f874072cab5dbe 394204 bedtools_2.16.1-1_powerpc.deb
+ 9f4317d029c006496afa0dbdc5fd3daafc730e72 412192 bedtools_2.17.0-1_powerpc.deb
Checksums-Sha256:
- 477f43437739d7e187998b7713b85fdaa067f39e293baf12db49323d6bfbf117 394204 bedtools_2.16.1-1_powerpc.deb
+ 0a65e3b8d342611b3b60b1bd59f93661333ea0d58f5343d69e16e24995b25f54 412192 bedtools_2.17.0-1_powerpc.deb
Files:
- c3c4eefa069d206a4fee80067d1f244d 394204 science optional bedtools_2.16.1-1_powerpc.deb
+ c33975f443920b33d83771a3a51f9174 412192 science optional bedtools_2.17.0-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_powerpc.deb
+bedtools_2.17.0-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 394204 bytes: control archive= 1976 bytes.
- 867 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 412192 bytes: control archive= 4111 bytes.
+ 32 bytes, 1 lines conffiles
+ 835 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1426
- 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)
+ Installed-Size: 1596
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -859,58 +877,168 @@ bedtools_2.16.1-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/bin/
--rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/intersectBed
--rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/nucBed
--rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/expandCols
--rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/mapBed
--rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/mergeBed
--rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/windowBed
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/bamToBed
--rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 36 2012-03-16 14:19 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/pairToBed
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/complementBed
--rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/closestBed
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/coverageBed
--rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/randomBed
--rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/clusterBed
--rwxr-xr-x root/root 29 2012-03-16 14:19 ./usr/bin/slopBed
--rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/pairToPair
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/bedToBam
--rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/linksBed
--rwxr-xr-x root/root 29 2012-03-16 14:19 ./usr/bin/sortBed
--rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/getOverlap
--rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/subtractBed
--rwxr-xr-x root/root 36 2012-03-16 14:19 ./usr/bin/windowMaker
--rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/flankBed
--rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/tagBam
--rwxr-xr-x root/root 1399248 2012-03-16 14:19 ./usr/bin/bedtools
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
-drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 14:14 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/bin/
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/linksBed
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/windowBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/nucBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 44 2012-11-04 11:35 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/complementBed
+-rwxr-xr-x root/root 37 2012-11-04 11:35 ./usr/bin/slopBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/tagBam
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 44 2012-11-04 11:35 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/expandCols
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/closestBed
+-rwxr-xr-x root/root 39 2012-11-04 11:35 ./usr/bin/randomBed
+-rwxr-xr-x root/root 1427928 2012-11-04 11:35 ./usr/bin/bedtools
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/mapBed
+-rwxr-xr-x root/root 36 2012-11-04 11:35 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 37 2012-11-04 11:35 ./usr/bin/sortBed
+-rwxr-xr-x root/root 38 2012-11-04 11:35 ./usr/bin/flankBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 40 2012-11-04 11:35 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 43 2012-11-04 11:35 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 42 2012-11-04 11:35 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:35 ./usr/bin/subtractBed
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:35 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -924,7 +1052,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-08cb5b0d-8010-4648-b47b-2b03c27aa4f0/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-39fd857a-c983-41c7-b40a-c4c564f04ace/build/buildd-bedtools_2.17.0-1-powerpc-P2ueRr
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -932,18 +1060,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 84380
-Build-Time: 308
+Build-Space: 86684
+Build-Time: 151
Distribution: sid
-Install-Time: 68
-Job: bedtools_2.16.1-1
+Install-Time: 84
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 417
-Source-Version: 2.16.1-1
-Space: 84380
+Package-Time: 254
+Source-Version: 2.17.0-1
+Space: 86684
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1420
-Build needed 00:06:57, 84380k disc space
+Finished at 20121104-1135
+Build needed 00:04:14, 86684k disc space
+Signature with key '9811BFE6' requested:
diff --git a/s390.log b/s390.log
index 1992c37..6c0ca69 100644
--- a/s390.log
+++ b/s390.log
@@ -1,71 +1,62 @@
-From buildd at zemlinsky.debian.org Fri Mar 16 12:26:44 2012
-Return-path: <buildd at zemlinsky.debian.org>
+From buildd at zandonai.debian.org Sun Nov 04 11:33:49 2012
+Return-path: <buildd at zandonai.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8WF1-0003k3-Mh
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:26:43 +0000
-Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1TUySb-0000z5-93
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:33:49 +0000
+Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zemlinsky.debian.org,
- EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8WF0-0005kx-Qb; Fri, 16 Mar 2012 12:26:42 +0000
-Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8WEz-0002Jz-QQ; Fri, 16 Mar 2012 12:26:41 +0000
-Message-Id: <E1S8WEz-0002Jz-QQ at zemlinsky.debian.org>
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1TUySa-000507-9q; Sun, 04 Nov 2012 11:33:48 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1TUySZ-0002W5-TQ; Sun, 04 Nov 2012 11:33:47 +0000
+Message-Id: <E1TUySZ-0002W5-TQ at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 12:26:41 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+Date: Sun, 4 Nov 2012 11:33:47 +0000
+From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on s390 (dist=sid)
-Key-Id: E0AC2C92
+Subject: Log for successful build of bedtools_2.17.0-1 on s390 (dist=sid)
+Key-Id: E7C67939
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (s390) 16 Mar 2012 12:22 ║
+║ bedtools 2.17.0-1 (s390) 04 Nov 2012 11:31 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: s390
-Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [198 kB]
-Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [6213 kB]
-Get:3 http://incoming.debian.org unstable InRelease [198 kB]
-Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [54.4 kB]
-Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
-Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390 Packages [5726 kB]
-Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390 Packages [36.7 kB]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2223 B]
-Get:9 http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en [37.1 kB]
-Get:10 http://ftp-stud.hs-esslingen.de unstable/main Translation-en [3902 kB]
+Hit http://ftp.de.debian.org unstable InRelease
+Hit http://ftp.de.debian.org unstable/main Sources
+Hit http://ftp.de.debian.org unstable/contrib Sources
+Hit http://ftp.de.debian.org unstable/non-free Sources
+Hit http://ftp.de.debian.org unstable/main s390 Packages
+Hit http://ftp.de.debian.org unstable/contrib s390 Packages
+Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get:11 http://incoming.debian.org Release.gpg [836 B]
-Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:15 http://incoming.debian.org unstable/main s390 Packages [5726 kB]
-Get:16 http://incoming.debian.org unstable/contrib s390 Packages [36.7 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:18 http://incoming.debian.org Release [1616 B]
-Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Get:21 http://incoming.debian.org Sources [59.8 kB]
-Get:22 http://incoming.debian.org Packages [692 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.3 MB in 11s (2825 kB/s)
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Hit http://incoming.debian.org unstable/non-free Sources
+Hit http://incoming.debian.org unstable/main s390 Packages
+Hit http://incoming.debian.org unstable/contrib s390 Packages
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release [1141 B]
+Get:3 http://incoming.debian.org Sources [16.2 kB]
+Get:4 http://incoming.debian.org Packages [140 kB]
+Fetched 158 kB in 2s (73.7 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (657 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 2s (449 kB/s)
Download complete and in download only mode
Check arch
@@ -104,58 +95,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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 (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-7)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.5-1)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-1.2)
-mount: already installed (2.20.1-1.2)
-util-linux: already installed (2.20.1-1.2)
-libc6-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -166,10 +157,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -179,165 +170,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 47 not upgraded.
-Need to get 17.9 MB of archives.
-After this operation, 49.4 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390 1:1.2.6.dfsg-2 [89.4 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390 5.9-4 [323 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390 1.0.0h-1 [1226 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390 5.10-1 [259 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390 2.30.2-6 [1875 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390 2.7.8.dfsg-7 [882 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390 0.6.4-2 [149 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390 2.0.1-7.2 [137 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390 4.8.30-11 [700 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390 9.0.1 [213 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390 2.6.1-1 [1068 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390 5.10-1 [53.5 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390 3.7.10-1 [456 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390 2.7.3~rc1-1 [1699 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390 2.7.3~rc1-1 [2661 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390 0.18.1.1-5 [2073 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390 1.55-2 [29.7 kB]
-Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390 1:1.2.6.dfsg-2 [213 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 45 not upgraded.
+Need to get 17.0 MB of archives.
+After this operation, 47.9 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libncursesw5 s390 5.9-10 [141 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.2-1 [40.6 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libssl1.0.0 s390 1.0.1c-4 [1259 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-9 [26.8 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 1:8.31-1 [253 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libsqlite3-0 s390 3.7.14.1-1 [476 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-6 [892 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.33.12+really2.32.4-3 [1785 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.6-1 [128 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libexpat1 s390 2.1.0-1 [140 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-9 [146 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.3-1 [1065 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main file s390 5.11-2 [52.0 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-9 [152 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main python2.7-minimal s390 2.7.3-5 [1700 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main python2.7 s390 2.7.3-5 [2691 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:27 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-9 [1959 kB]
+Get:28 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
+Get:32 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.9 MB in 1s (17.1 MB/s)
-(Reading database ... 10800 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10800 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_s390.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_s390.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_s390.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390.deb) ...
+Fetched 17.0 MB in 7s (2149 kB/s)
+Selecting previously unselected package libncursesw5:s390.
+(Reading database ... 10684 files and directories currently installed.)
+Unpacking libncursesw5:s390 (from .../libncursesw5_5.9-10_s390.deb) ...
+Selecting previously unselected package libpipeline1:s390.
+Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.2-1_s390.deb) ...
+Selecting previously unselected package libssl1.0.0:s390.
+Unpacking libssl1.0.0:s390 (from .../libssl1.0.0_1.0.1c-4_s390.deb) ...
+Selecting previously unselected package libasprintf0c2:s390.
+Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-9_s390.deb) ...
+Selecting previously unselected package libmagic1:s390.
+Unpacking libmagic1:s390 (from .../libmagic1_5.11-2_s390.deb) ...
+Selecting previously unselected package libpcre3:s390.
+Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.31-1_s390.deb) ...
+Selecting previously unselected package libsqlite3-0:s390.
+Unpacking libsqlite3-0:s390 (from .../libsqlite3-0_3.7.14.1-1_s390.deb) ...
+Selecting previously unselected package libxml2:s390.
+Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-6_s390.deb) ...
+Selecting previously unselected package libffi5:s390.
+Unpacking libffi5:s390 (from .../libffi5_3.0.10-3_s390.deb) ...
+Selecting previously unselected package libglib2.0-0:s390.
+Unpacking libglib2.0-0:s390 (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390.deb) ...
+Selecting previously unselected package libcroco3:s390.
+Unpacking libcroco3:s390 (from .../libcroco3_0.6.6-1_s390.deb) ...
+Selecting previously unselected package libexpat1:s390.
+Unpacking libexpat1:s390 (from .../libexpat1_2.1.0-1_s390.deb) ...
+Selecting previously unselected package libunistring0:s390.
+Unpacking libunistring0:s390 (from .../libunistring0_0.9.3-5_s390.deb) ...
+Selecting previously unselected package libgettextpo0:s390.
+Unpacking libgettextpo0:s390 (from .../libgettextpo0_0.18.1.1-9_s390.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_s390.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_s390.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_s390.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_s390.deb) ...
+Unpacking file (from .../archives/file_5.11-2_s390.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_s390.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_s390.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_s390.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_s390.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_s390.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_s390.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:s390.
+Unpacking zlib1g-dev:s390 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390.deb) ...
+Setting up libncursesw5:s390 (5.9-10) ...
+Setting up libpipeline1:s390 (1.2.2-1) ...
+Setting up libssl1.0.0:s390 (1.0.1c-4) ...
+Setting up libasprintf0c2:s390 (0.18.1.1-9) ...
+Setting up libmagic1:s390 (5.11-2) ...
+Setting up libpcre3:s390 (1:8.31-1) ...
+Setting up libsqlite3-0:s390 (3.7.14.1-1) ...
+Setting up libxml2:s390 (2.8.0+dfsg1-6) ...
+Setting up libffi5:s390 (3.0.10-3) ...
+Setting up libglib2.0-0:s390 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:s390 (0.6.6-1) ...
+Setting up libexpat1:s390 (2.1.0-1) ...
+Setting up libunistring0:s390 (0.9.3-5) ...
+Setting up libgettextpo0:s390 (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:s390 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 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_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 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_3.11 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_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 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_1:4.6.2-14 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 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 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 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_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-2 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -348,12 +337,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -364,18 +353,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture s390
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -391,11 +380,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -403,30 +392,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -437,7 +428,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -512,7 +503,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -521,7 +512,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -571,10 +562,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -597,6 +591,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -640,7 +635,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -664,7 +659,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -678,6 +673,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -751,16 +747,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0'
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
@@ -776,8 +794,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-s390-Hwm_nv/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -787,66 +808,70 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.17.0-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1226
+Build finished at 20121104-1133
-bedtools_2.16.1-1_s390.changes:
+bedtools_2.17.0-1_s390.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- a51394a8cee66cc0e0469d100b641b38a89b7d97 388520 bedtools_2.16.1-1_s390.deb
+ df49331644d3d3657db5efd6eda32935275a3ea9 407892 bedtools_2.17.0-1_s390.deb
Checksums-Sha256:
- 60f37bcf3e7a6ec0ade5d7de8f5d9dd881316edc7f4779f2ee8a4190f27599e1 388520 bedtools_2.16.1-1_s390.deb
+ b685a8b7ad2949d24f1f65ef002d76b36835c92c6d464341b9c26511d7d09946 407892 bedtools_2.17.0-1_s390.deb
Files:
- 8bbfd52d792de3aa5e84e86bbefac711 388520 science optional bedtools_2.16.1-1_s390.deb
+ f819594f017a84f8fa94d3de20a5d1bf 407892 science optional bedtools_2.17.0-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_s390.deb
+bedtools_2.17.0-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 388520 bytes: control archive= 1975 bytes.
- 864 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 407892 bytes: control archive= 4100 bytes.
+ 32 bytes, 1 lines conffiles
+ 832 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1394
- 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)
+ Installed-Size: 1564
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -860,58 +885,168 @@ bedtools_2.16.1-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:22 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/bin/
--rwxr-xr-x root/root 36 2012-03-16 12:26 ./usr/bin/windowMaker
--rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/pairToBed
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/bamToBed
--rwxr-xr-x root/root 29 2012-03-16 12:26 ./usr/bin/slopBed
--rwxr-xr-x root/root 1366148 2012-03-16 12:26 ./usr/bin/bedtools
--rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/mapBed
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/subtractBed
--rwxr-xr-x root/root 29 2012-03-16 12:26 ./usr/bin/sortBed
--rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/flankBed
--rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/annotateBed
--rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/windowBed
--rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/clusterBed
--rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/nucBed
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/bedToBam
--rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/getOverlap
--rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 36 2012-03-16 12:26 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/expandCols
--rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/closestBed
--rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/complementBed
--rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/randomBed
--rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/pairToPair
--rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/tagBam
--rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/coverageBed
--rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/intersectBed
--rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/bin/
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 38 2012-11-04 11:33 ./usr/bin/linksBed
+-rwxr-xr-x root/root 40 2012-11-04 11:33 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 39 2012-11-04 11:33 ./usr/bin/windowBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-11-04 11:33 ./usr/bin/mapBed
+-rwxr-xr-x root/root 36 2012-11-04 11:33 ./usr/bin/tagBam
+-rwxr-xr-x root/root 38 2012-11-04 11:33 ./usr/bin/flankBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 43 2012-11-04 11:33 ./usr/bin/complementBed
+-rwxr-xr-x root/root 42 2012-11-04 11:33 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 40 2012-11-04 11:33 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 11:33 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 1394828 2012-11-04 11:33 ./usr/bin/bedtools
+-rwxr-xr-x root/root 42 2012-11-04 11:33 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 42 2012-11-04 11:33 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 42 2012-11-04 11:33 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 44 2012-11-04 11:33 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 39 2012-11-04 11:33 ./usr/bin/expandCols
+-rwxr-xr-x root/root 43 2012-11-04 11:33 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 44 2012-11-04 11:33 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 38 2012-11-04 11:33 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 36 2012-11-04 11:33 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 43 2012-11-04 11:33 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 43 2012-11-04 11:33 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 40 2012-11-04 11:33 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 36 2012-11-04 11:33 ./usr/bin/nucBed
+-rwxr-xr-x root/root 40 2012-11-04 11:33 ./usr/bin/closestBed
+-rwxr-xr-x root/root 41 2012-11-04 11:33 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 42 2012-11-04 11:33 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 37 2012-11-04 11:33 ./usr/bin/sortBed
+-rwxr-xr-x root/root 37 2012-11-04 11:33 ./usr/bin/slopBed
+-rwxr-xr-x root/root 39 2012-11-04 11:33 ./usr/bin/randomBed
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+drwxr-xr-x root/root 0 2012-11-04 11:31 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:33 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -925,7 +1060,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-53766b8b-5bdd-44cf-bca9-514ab6d33688/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX
+Purging /var/lib/schroot/mount/sid-s390-sbuild-83c05a5d-30f1-4614-b61d-2ef7f9680845/build/buildd-bedtools_2.17.0-1-s390-Hwm_nv
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -933,89 +1068,80 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 89552
-Build-Time: 232
+Build-Space: 93040
+Build-Time: 131
Distribution: sid
-Install-Time: 21
-Job: bedtools_2.16.1-1
+Install-Time: 16
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 272
-Source-Version: 2.16.1-1
-Space: 89552
+Package-Time: 162
+Source-Version: 2.17.0-1
+Space: 93040
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1226
-Build needed 00:04:32, 89552k disc space
-Signature with key 'E0AC2C92' requested:
-From buildd at zemlinsky.debian.org Fri Mar 16 12:18:42 2012
+Finished at 20121104-1133
+Build needed 00:02:42, 93040k disc space
+Signature with key 'E7C67939' requested:
+From buildd at zemlinsky.debian.org Sun Nov 04 11:36:33 2012
Return-path: <buildd at zemlinsky.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7G-00029z-7n
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:18:42 +0000
+ id 1TUyVF-0001W5-G7
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:36:33 +0000
Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zemlinsky.debian.org,
EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7F-00057G-AL; Fri, 16 Mar 2012 12:18:41 +0000
+ id 1TUyVE-0005N0-EK; Sun, 04 Nov 2012 11:36:32 +0000
Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
(envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7F-0003Xc-5i; Fri, 16 Mar 2012 12:18:41 +0000
-Message-Id: <E1S8W7F-0003Xc-5i at zemlinsky.debian.org>
+ id 1TUyVD-0007CR-Sh; Sun, 04 Nov 2012 11:36:31 +0000
+Message-Id: <E1TUyVD-0007CR-Sh at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 12:18:41 +0000
+Date: Sun, 4 Nov 2012 11:36:31 +0000
From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
-To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on s390x (dist=sid)
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on s390x (dist=sid)
Key-Id: 6A3F7E2B
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (s390x) 16 Mar 2012 12:14 ║
+║ bedtools 2.17.0-1 (s390x) 04 Nov 2012 11:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: s390x
Hit http://ftp-stud.hs-esslingen.de unstable InRelease
Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
-Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Hit http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
-Hit http://ftp-stud.hs-esslingen.de unstable/main Translation-en
Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
Hit http://incoming.debian.org unstable/main Sources
Hit http://incoming.debian.org unstable/contrib Sources
-Get:3 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
Hit http://incoming.debian.org unstable/main s390x Packages
Hit http://incoming.debian.org unstable/contrib s390x Packages
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Hit http://incoming.debian.org unstable/main TranslationIndex
-Get:4 http://incoming.debian.org Release [1616 B]
-Hit http://incoming.debian.org unstable/contrib Translation-en
-Hit http://incoming.debian.org unstable/main Translation-en
-Get:5 http://incoming.debian.org Sources [58.9 kB]
-Get:6 http://incoming.debian.org Packages [687 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 948 kB in 2s (446 kB/s)
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org Sources [16.2 kB]
+Get:6 http://incoming.debian.org Packages [140 kB]
+Fetched 361 kB in 1s (192 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1035,12 +1161,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (611 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (657 kB/s)
Download complete and in download only mode
Check arch
@@ -1054,34 +1180,34 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5+b1)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1+b1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -1092,10 +1218,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -1105,165 +1231,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 46 not upgraded.
-Need to get 18.1 MB of archives.
-After this operation, 51.5 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390x 1:1.2.6.dfsg-2 [91.1 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.0h-1 [1224 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.10-1 [255 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-6 [1867 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-7 [894 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.4-2 [150 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.1 [214 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.1-1 [1070 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.10-1 [53.6 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.10-1 [448 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3~rc1-1 [1744 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3~rc1-1 [2677 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 44 not upgraded.
+Need to get 17.2 MB of archives.
+After this operation, 50.3 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-10 [144 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.1c-4 [1259 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.14.1-1 [468 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-6 [901 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-1 [129 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.1.0-1 [144 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-1 [1071 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3-5 [1747 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3-5 [2702 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.6.dfsg-2 [217 kB]
+Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.1 MB in 1s (9669 kB/s)
-(Reading database ... 10788 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390x.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10788 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390x.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390x.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_s390x.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390x.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390x.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390x.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390x.deb) ...
+Fetched 17.2 MB in 2s (7351 kB/s)
+Selecting previously unselected package libncursesw5:s390x.
+(Reading database ... 10810 files and directories currently installed.)
+Unpacking libncursesw5:s390x (from .../libncursesw5_5.9-10_s390x.deb) ...
+Selecting previously unselected package libpipeline1:s390x.
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+Selecting previously unselected package libssl1.0.0:s390x.
+Unpacking libssl1.0.0:s390x (from .../libssl1.0.0_1.0.1c-4_s390x.deb) ...
+Selecting previously unselected package libasprintf0c2:s390x.
+Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package libmagic1:s390x.
+Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Selecting previously unselected package libpcre3:s390x.
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
+Selecting previously unselected package libsqlite3-0:s390x.
+Unpacking libsqlite3-0:s390x (from .../libsqlite3-0_3.7.14.1-1_s390x.deb) ...
+Selecting previously unselected package libxml2:s390x.
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-6_s390x.deb) ...
+Selecting previously unselected package libffi5:s390x.
+Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
+Selecting previously unselected package libglib2.0-0:s390x.
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
+Selecting previously unselected package libcroco3:s390x.
+Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-1_s390x.deb) ...
+Selecting previously unselected package libexpat1:s390x.
+Unpacking libexpat1:s390x (from .../libexpat1_2.1.0-1_s390x.deb) ...
+Selecting previously unselected package libunistring0:s390x.
+Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libgettextpo0:s390x.
+Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6+b1_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_s390x.deb) ...
+Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390x.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390x.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_s390x.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390x.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_s390x.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5+b1_s390x.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390x.deb) ...
-Setting up libncursesw5 (5.9-4+b1) ...
-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+b1) ...
-Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:s390x.
+Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
+Setting up libncursesw5:s390x (5.9-10) ...
+Setting up libpipeline1:s390x (1.2.2-1) ...
+Setting up libssl1.0.0:s390x (1.0.1c-4) ...
+Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
+Setting up libmagic1:s390x (5.11-2) ...
+Setting up libpcre3:s390x (1:8.31-1) ...
+Setting up libsqlite3-0:s390x (3.7.14.1-1) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-6) ...
+Setting up libffi5:s390x (3.0.10-3+b1) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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+b1) ...
-Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:s390x (0.6.6-1) ...
+Setting up libexpat1:s390x (2.1.0-1) ...
+Setting up libunistring0:s390x (0.9.3-5+b1) ...
+Setting up libgettextpo0:s390x (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5+b1) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-5+b1) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
-Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 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_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.11 html2text_1.3.2a-15+b1 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_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 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+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-14 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 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+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1+b1 man-db_2.6.1-1 mawk_1.3.3-16+b1 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 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 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1274,12 +1398,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1290,18 +1414,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture s390x
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -1317,11 +1441,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1329,30 +1453,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -1363,7 +1489,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -1442,7 +1568,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -1451,7 +1577,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -1501,10 +1627,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -1527,6 +1656,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -1570,7 +1700,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -1594,7 +1724,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -1608,6 +1738,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -1681,16 +1812,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
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
@@ -1706,8 +1859,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -1717,27 +1873,27 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390x.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.17.0-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1218
+Build finished at 20121104-1136
-bedtools_2.16.1-1_s390x.changes:
+bedtools_2.17.0-1_s390x.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
@@ -1745,38 +1901,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 424cae8f7eead80d7cde6b6e5ff19bbb341002af 439128 bedtools_2.16.1-1_s390x.deb
+ ad9c92ce690adb264c4f552c32926fa231b8543e 458538 bedtools_2.17.0-1_s390x.deb
Checksums-Sha256:
- 152d71f6e27f61b20bc49d0a888a243dcac5643582a16170670900b3dfd8620d 439128 bedtools_2.16.1-1_s390x.deb
+ 9e879db814882792a2047e2f87908db888ee3d04a12f077ce251d5f23a3a00a8 458538 bedtools_2.17.0-1_s390x.deb
Files:
- ac4b1186a2ef597687c0e5c823a25624 439128 science optional bedtools_2.16.1-1_s390x.deb
+ 5cb3cb78aa7b4ff5dc8140a8188817da 458538 science optional bedtools_2.17.0-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_s390x.deb
+bedtools_2.17.0-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 439128 bytes: control archive= 1980 bytes.
- 866 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 458538 bytes: control archive= 4106 bytes.
+ 32 bytes, 1 lines conffiles
+ 834 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1604
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1777
+ Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -1790,58 +1950,168 @@ bedtools_2.16.1-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:14 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/bin/
--rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/windowMaker
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/pairToBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bamToBed
--rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/slopBed
--rwxr-xr-x root/root 1580616 2012-03-16 12:18 ./usr/bin/bedtools
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/mapBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/subtractBed
--rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/sortBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/flankBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/annotateBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/windowBed
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/clusterBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/nucBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bedToBam
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/getOverlap
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/expandCols
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/closestBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/complementBed
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/randomBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/pairToPair
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/tagBam
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/coverageBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/intersectBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/bin/
+-rwxr-xr-x root/root 44 2012-11-04 11:36 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 37 2012-11-04 11:36 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1613400 2012-11-04 11:36 ./usr/bin/bedtools
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/mapBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 37 2012-11-04 11:36 ./usr/bin/sortBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/flankBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/windowBed
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/nucBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 44 2012-11-04 11:36 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/expandCols
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/closestBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/complementBed
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/randomBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/linksBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/tagBam
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1855,7 +2125,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-2aaa36e6-7015-4003-a01a-abc96f7363b0/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-e7105a7b-c4bd-42e9-b131-51e513ead6f2/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1863,18 +2133,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 125844
-Build-Time: 235
+Build-Space: 129412
+Build-Time: 238
Distribution: sid
Install-Time: 21
-Job: bedtools_2.16.1-1
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 265
-Source-Version: 2.16.1-1
-Space: 125844
+Package-Time: 269
+Source-Version: 2.17.0-1
+Space: 129412
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1218
-Build needed 00:04:25, 125844k disc space
+Finished at 20121104-1136
+Build needed 00:04:29, 129412k disc space
Signature with key '6A3F7E2B' requested:
diff --git a/s390x.log b/s390x.log
index c637308..6661869 100644
--- a/s390x.log
+++ b/s390x.log
@@ -1,71 +1,62 @@
-From buildd at zemlinsky.debian.org Fri Mar 16 12:18:42 2012
+From buildd at zemlinsky.debian.org Sun Nov 04 11:36:33 2012
Return-path: <buildd at zemlinsky.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7G-00029z-7n
- for logs at buildd.debian.org; Fri, 16 Mar 2012 12:18:42 +0000
+ id 1TUyVF-0001W5-G7
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:36:33 +0000
Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zemlinsky.debian.org,
EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7F-00057G-AL; Fri, 16 Mar 2012 12:18:41 +0000
+ id 1TUyVE-0005N0-EK; Sun, 04 Nov 2012 11:36:32 +0000
Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
(envelope-from <buildd at zemlinsky.debian.org>)
- id 1S8W7F-0003Xc-5i; Fri, 16 Mar 2012 12:18:41 +0000
-Message-Id: <E1S8W7F-0003Xc-5i at zemlinsky.debian.org>
+ id 1TUyVD-0007CR-Sh; Sun, 04 Nov 2012 11:36:31 +0000
+Message-Id: <E1TUyVD-0007CR-Sh at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 12:18:41 +0000
+Date: Sun, 4 Nov 2012 11:36:31 +0000
From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
-To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on s390x (dist=sid)
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on s390x (dist=sid)
Key-Id: 6A3F7E2B
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (s390x) 16 Mar 2012 12:14 ║
+║ bedtools 2.17.0-1 (s390x) 04 Nov 2012 11:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: s390x
Hit http://ftp-stud.hs-esslingen.de unstable InRelease
Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
-Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Hit http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
-Hit http://ftp-stud.hs-esslingen.de unstable/main Translation-en
Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
Hit http://incoming.debian.org unstable/main Sources
Hit http://incoming.debian.org unstable/contrib Sources
-Get:3 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
Hit http://incoming.debian.org unstable/main s390x Packages
Hit http://incoming.debian.org unstable/contrib s390x Packages
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Hit http://incoming.debian.org unstable/main TranslationIndex
-Get:4 http://incoming.debian.org Release [1616 B]
-Hit http://incoming.debian.org unstable/contrib Translation-en
-Hit http://incoming.debian.org unstable/main Translation-en
-Get:5 http://incoming.debian.org Sources [58.9 kB]
-Get:6 http://incoming.debian.org Packages [687 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 948 kB in 2s (446 kB/s)
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org Sources [16.2 kB]
+Get:6 http://incoming.debian.org Packages [140 kB]
+Fetched 361 kB in 1s (192 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 1s (611 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (657 kB/s)
Download complete and in download only mode
Check arch
@@ -104,34 +95,34 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5+b1)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-26)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1+b1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -142,10 +133,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal zlib1g
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -155,165 +146,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-The following packages will be upgraded:
- zlib1g
-1 upgraded, 32 newly installed, 0 to remove and 46 not upgraded.
-Need to get 18.1 MB of archives.
-After this operation, 51.5 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390x 1:1.2.6.dfsg-2 [91.1 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.0h-1 [1224 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.10-1 [255 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-6 [1867 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-7 [894 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.4-2 [150 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.1 [214 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.1-1 [1070 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.10-1 [53.6 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.10-1 [448 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3~rc1-1 [1744 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3~rc1-1 [2677 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 44 not upgraded.
+Need to get 17.2 MB of archives.
+After this operation, 50.3 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-10 [144 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.1c-4 [1259 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.14.1-1 [468 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-6 [901 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-1 [129 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.1.0-1 [144 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-1 [1071 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3-5 [1747 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3-5 [2702 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.6.dfsg-2 [217 kB]
+Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.1 MB in 1s (9669 kB/s)
-(Reading database ... 10788 files and directories currently installed.)
-Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390x.deb) ...
-Unpacking replacement zlib1g ...
-Setting up zlib1g (1:1.2.6.dfsg-2) ...
-Selecting previously unselected package libncursesw5.
-(Reading database ... 10788 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390x.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390x.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_s390x.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390x.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390x.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390x.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390x.deb) ...
+Fetched 17.2 MB in 2s (7351 kB/s)
+Selecting previously unselected package libncursesw5:s390x.
+(Reading database ... 10810 files and directories currently installed.)
+Unpacking libncursesw5:s390x (from .../libncursesw5_5.9-10_s390x.deb) ...
+Selecting previously unselected package libpipeline1:s390x.
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+Selecting previously unselected package libssl1.0.0:s390x.
+Unpacking libssl1.0.0:s390x (from .../libssl1.0.0_1.0.1c-4_s390x.deb) ...
+Selecting previously unselected package libasprintf0c2:s390x.
+Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
+Selecting previously unselected package libmagic1:s390x.
+Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Selecting previously unselected package libpcre3:s390x.
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
+Selecting previously unselected package libsqlite3-0:s390x.
+Unpacking libsqlite3-0:s390x (from .../libsqlite3-0_3.7.14.1-1_s390x.deb) ...
+Selecting previously unselected package libxml2:s390x.
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-6_s390x.deb) ...
+Selecting previously unselected package libffi5:s390x.
+Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
+Selecting previously unselected package libglib2.0-0:s390x.
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
+Selecting previously unselected package libcroco3:s390x.
+Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-1_s390x.deb) ...
+Selecting previously unselected package libexpat1:s390x.
+Unpacking libexpat1:s390x (from .../libexpat1_2.1.0-1_s390x.deb) ...
+Selecting previously unselected package libunistring0:s390x.
+Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libgettextpo0:s390x.
+Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6+b1_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_s390x.deb) ...
+Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390x.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390x.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_s390x.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390x.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_s390x.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5+b1_s390x.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390x.deb) ...
-Setting up libncursesw5 (5.9-4+b1) ...
-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+b1) ...
-Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:s390x.
+Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
+Setting up libncursesw5:s390x (5.9-10) ...
+Setting up libpipeline1:s390x (1.2.2-1) ...
+Setting up libssl1.0.0:s390x (1.0.1c-4) ...
+Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
+Setting up libmagic1:s390x (5.11-2) ...
+Setting up libpcre3:s390x (1:8.31-1) ...
+Setting up libsqlite3-0:s390x (3.7.14.1-1) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-6) ...
+Setting up libffi5:s390x (3.0.10-3+b1) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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+b1) ...
-Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:s390x (0.6.6-1) ...
+Setting up libexpat1:s390x (2.1.0-1) ...
+Setting up libunistring0:s390x (0.9.3-5+b1) ...
+Setting up libgettextpo0:s390x (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5+b1) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-5+b1) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 44 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
-Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 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_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.11 html2text_1.3.2a-15+b1 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_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 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+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-14 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 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+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1+b1 man-db_2.6.1-1 mawk_1.3.3-16+b1 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 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 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -324,12 +313,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -340,18 +329,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture s390x
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -367,11 +356,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -379,30 +368,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -413,7 +404,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -492,7 +483,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -501,7 +492,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -551,10 +542,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -577,6 +571,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -620,7 +615,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -644,7 +639,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -658,6 +653,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -731,16 +727,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
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 '/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+ cd '/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0'
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
@@ -756,8 +774,11 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
@@ -767,27 +788,27 @@ dh_gencontrol -pbedtools
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390x.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.17.0-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1218
+Build finished at 20121104-1136
-bedtools_2.16.1-1_s390x.changes:
+bedtools_2.17.0-1_s390x.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
@@ -795,38 +816,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 424cae8f7eead80d7cde6b6e5ff19bbb341002af 439128 bedtools_2.16.1-1_s390x.deb
+ ad9c92ce690adb264c4f552c32926fa231b8543e 458538 bedtools_2.17.0-1_s390x.deb
Checksums-Sha256:
- 152d71f6e27f61b20bc49d0a888a243dcac5643582a16170670900b3dfd8620d 439128 bedtools_2.16.1-1_s390x.deb
+ 9e879db814882792a2047e2f87908db888ee3d04a12f077ce251d5f23a3a00a8 458538 bedtools_2.17.0-1_s390x.deb
Files:
- ac4b1186a2ef597687c0e5c823a25624 439128 science optional bedtools_2.16.1-1_s390x.deb
+ 5cb3cb78aa7b4ff5dc8140a8188817da 458538 science optional bedtools_2.17.0-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_s390x.deb
+bedtools_2.17.0-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 439128 bytes: control archive= 1980 bytes.
- 866 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 458538 bytes: control archive= 4106 bytes.
+ 32 bytes, 1 lines conffiles
+ 834 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1604
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1777
+ Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -840,58 +865,168 @@ bedtools_2.16.1-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 12:14 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/bin/
--rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/windowMaker
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/pairToBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bamToBed
--rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/slopBed
--rwxr-xr-x root/root 1580616 2012-03-16 12:18 ./usr/bin/bedtools
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/mapBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/subtractBed
--rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/sortBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/flankBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bedpeToBam
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/annotateBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/windowBed
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/clusterBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/nucBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bedToBam
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/getOverlap
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/mergeBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/expandCols
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/closestBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/complementBed
--rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/randomBed
--rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/linksBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/pairToPair
--rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/tagBam
--rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/coverageBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/intersectBed
--rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/jaccard/
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/flank/
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/coverage/
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./usr/bin/
+-rwxr-xr-x root/root 44 2012-11-04 11:36 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 37 2012-11-04 11:36 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1613400 2012-11-04 11:36 ./usr/bin/bedtools
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/mapBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 37 2012-11-04 11:36 ./usr/bin/sortBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/flankBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/windowBed
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/nucBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 44 2012-11-04 11:36 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/expandCols
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/closestBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/complementBed
+-rwxr-xr-x root/root 39 2012-11-04 11:36 ./usr/bin/randomBed
+-rwxr-xr-x root/root 38 2012-11-04 11:36 ./usr/bin/linksBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 40 2012-11-04 11:36 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 36 2012-11-04 11:36 ./usr/bin/tagBam
+-rwxr-xr-x root/root 43 2012-11-04 11:36 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:36 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 42 2012-11-04 11:36 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:36 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -905,7 +1040,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-2aaa36e6-7015-4003-a01a-abc96f7363b0/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-e7105a7b-c4bd-42e9-b131-51e513ead6f2/build/buildd-bedtools_2.17.0-1-s390x-a1TXHZ
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -913,18 +1048,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 125844
-Build-Time: 235
+Build-Space: 129412
+Build-Time: 238
Distribution: sid
Install-Time: 21
-Job: bedtools_2.16.1-1
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 265
-Source-Version: 2.16.1-1
-Space: 125844
+Package-Time: 269
+Source-Version: 2.17.0-1
+Space: 129412
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1218
-Build needed 00:04:25, 125844k disc space
+Finished at 20121104-1136
+Build needed 00:04:29, 129412k disc space
Signature with key '6A3F7E2B' requested:
diff --git a/sparc.log b/sparc.log
index 8299a1a..f9e9c2e 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,72 +1,62 @@
-From buildd at schroeder.debian.org Fri Mar 16 13:41:03 2012
-Return-path: <buildd at schroeder.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at lebrun.debian.org Sun Nov 04 11:45:52 2012
+Return-path: <buildd at lebrun.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1S8XOx-0001qS-BO
- for logs at buildd.debian.org; Fri, 16 Mar 2012 13:41:03 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1TUyeG-0002op-Ak
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:45:52 +0000
+Received: from [2001:b68:ff:5:203:baff:fe59:abad] (helo=lebrun.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=schroeder.debian.org,
- EMAIL=hostmaster at schroeder.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1S8XOw-0002w1-AP
- for logs at buildd.debian.org; Fri, 16 Mar 2012 13:41:02 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.72)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1S8XOu-00029p-FT; Fri, 16 Mar 2012 13:41:00 +0000
-Message-Id: <E1S8XOu-00029p-FT at schroeder.debian.org>
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1TUyeF-00063n-7i
+ for logs at buildd.debian.org; Sun, 04 Nov 2012 11:45:51 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1TUyeC-0001sX-Lt; Sun, 04 Nov 2012 11:45:48 +0000
+Message-Id: <E1TUyeC-0001sX-Lt at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 16 Mar 2012 13:41:00 +0000
-From: buildd on schroeder <buildd at schroeder.debian.org>
-To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
-Subject: Log for successful build of bedtools_2.16.1-1 on sparc (dist=sid)
-Key-Id: 24E4F805
+Date: Sun, 4 Nov 2012 11:45:48 +0000
+From: buildd on lebrun <buildd at lebrun.debian.org>
+To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
+Subject: Log for successful build of bedtools_2.17.0-1 on sparc (dist=sid)
+Key-Id: E1D842D6
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.16.1-1 (sparc) 16 Mar 2012 13:25 ║
+║ bedtools 2.17.0-1 (sparc) 04 Nov 2012 11:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.16.1-1
-Source Version: 2.16.1-1
+Version: 2.17.0-1
+Source Version: 2.17.0-1
Architecture: sparc
-Get:1 http://ftp.hr.debian.org unstable InRelease [198 kB]
-Get:2 http://incoming.debian.org unstable InRelease [198 kB]
-Get:3 http://ftp.hr.debian.org unstable/main Sources [6213 kB]
-Get:4 http://ftp.hr.debian.org unstable/contrib Sources [54.4 kB]
-Get:5 http://ftp.hr.debian.org unstable/non-free Sources [99.8 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [219 kB]
+Get:2 http://incoming.debian.org unstable InRelease [219 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [6381 kB]
Ign http://incoming.debian.org InRelease
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://ftp.hr.debian.org unstable/main sparc Packages [5777 kB]
-Get:8 http://incoming.debian.org Release [1616 B]
-Get:9 http://incoming.debian.org unstable/main Sources [6213 kB]
-Get:10 http://ftp.hr.debian.org unstable/contrib sparc Packages [36.9 kB]
-Ign http://ftp.hr.debian.org unstable/contrib TranslationIndex
-Get:11 http://ftp.hr.debian.org unstable/main TranslationIndex [2223 B]
-Get:12 http://ftp.hr.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:13 http://ftp.hr.debian.org unstable/main Translation-en [3902 kB]
-Get:14 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
-Get:15 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
-Get:16 http://incoming.debian.org unstable/main sparc Packages [5777 kB]
-Get:17 http://incoming.debian.org unstable/contrib sparc Packages [36.9 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:18 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
-Get:19 http://incoming.debian.org Sources [61.1 kB]
-Get:20 http://incoming.debian.org Packages [697 kB]
-Get:21 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
-Get:22 http://incoming.debian.org unstable/main Translation-en [3902 kB]
-Ign http://incoming.debian.org Translation-en
-Fetched 33.4 MB in 34s (972 kB/s)
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6381 kB]
+Get:6 http://debian.carnet.hr unstable/contrib Sources [53.1 kB]
+Get:7 http://debian.carnet.hr unstable/non-free Sources [101 kB]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [6043 kB]
+Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [36.9 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [53.1 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main sparc Packages [6043 kB]
+Get:13 http://incoming.debian.org unstable/contrib sparc Packages [36.9 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [16.2 kB]
+Get:16 http://incoming.debian.org Packages [140 kB]
+Fetched 25.8 MB in 60s (429 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/git/debian-med/bedtools.git
-Need to get 985 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
-Fetched 985 kB in 3s (327 kB/s)
+git://git.debian.org/debian-med/bedtools.git
+Need to get 1216 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (dsc) [1951 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (tar) [1209 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.17.0-1 (diff) [5663 B]
+Fetched 1216 kB in 1s (621 kB/s)
Download complete and in download only mode
Check arch
@@ -105,59 +95,59 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.2-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
+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, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 9), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.7)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.2.1)
-diffutils: already installed (1:3.2-2)
-dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42.1-2)
+debianutils: already installed (4.3.3)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
-grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
+grep: already installed (2.12-2)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-4)
-ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-9)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.5-1)
-sysvinit-utils: already installed (2.88dsf-22)
-sysvinit: already installed (2.88dsf-22)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-4)
-mount: already installed (2.20.1-4)
-util-linux: already installed (2.20.1-4)
-libc6-dev: already installed (2.13-27)
-libc6-dev-sparc64: already installed (2.13-27)
-gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+libc6-dev-sparc64: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 9.20120312
+Using default version 9.20120909
quilt: missing
python: missing
zlib1g-dev: missing
@@ -168,10 +158,10 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
- libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
- libxml2 man-db mime-support po-debconf python-minimal python2.7
- python2.7-minimal
+ intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0
+ libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -181,158 +171,163 @@ Recommended packages:
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
- libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
- libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
- python2.7 python2.7-minimal quilt zlib1g-dev
-0 upgraded, 32 newly installed, 0 to remove and 10 not upgraded.
-Need to get 16.9 MB of archives.
-After this operation, 47.8 MB of additional disk space will be used.
-Get:1 http://ftp.hr.debian.org/debian/ unstable/main libncursesw5 sparc 5.9-4 [302 kB]
-Get:2 http://ftp.hr.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
-Get:3 http://ftp.hr.debian.org/debian/ unstable/main libssl1.0.0 sparc 1.0.0h-1 [1052 kB]
-Get:4 http://ftp.hr.debian.org/debian/ unstable/main libmagic1 sparc 5.10-1 [248 kB]
-Get:5 http://ftp.hr.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:6 http://ftp.hr.debian.org/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
-Get:7 http://ftp.hr.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.30.2-6 [1694 kB]
-Get:8 http://ftp.hr.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-7 [819 kB]
-Get:9 http://ftp.hr.debian.org/debian/ unstable/main libcroco3 sparc 0.6.4-2 [135 kB]
-Get:10 http://ftp.hr.debian.org/debian/ unstable/main libexpat1 sparc 2.0.1-7.2 [128 kB]
-Get:11 http://ftp.hr.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:12 http://ftp.hr.debian.org/debian/ unstable/main libdb4.8 sparc 4.8.30-11 [639 kB]
-Get:13 http://ftp.hr.debian.org/debian/ unstable/main bsdmainutils sparc 9.0.1 [205 kB]
-Get:14 http://ftp.hr.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:15 http://ftp.hr.debian.org/debian/ unstable/main man-db sparc 2.6.1-1 [1039 kB]
-Get:16 http://ftp.hr.debian.org/debian/ unstable/main file sparc 5.10-1 [52.5 kB]
-Get:17 http://ftp.hr.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
-Get:18 http://ftp.hr.debian.org/debian/ unstable/main libsqlite3-0 sparc 3.7.10-1 [406 kB]
-Get:19 http://ftp.hr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
-Get:20 http://ftp.hr.debian.org/debian/ unstable/main python2.7-minimal sparc 2.7.3~rc1-1 [1600 kB]
-Get:21 http://ftp.hr.debian.org/debian/ unstable/main python2.7 sparc 2.7.3~rc1-1 [2588 kB]
-Get:22 http://ftp.hr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
-Get:23 http://ftp.hr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
-Get:24 http://ftp.hr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
-Get:25 http://ftp.hr.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:26 http://ftp.hr.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
-Get:27 http://ftp.hr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:28 http://ftp.hr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:29 http://ftp.hr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
-Get:30 http://ftp.hr.debian.org/debian/ unstable/main diffstat sparc 1.55-2 [28.4 kB]
-Get:31 http://ftp.hr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:32 http://ftp.hr.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.6.dfsg-2 [209 kB]
+ html2text intltool-debian libasprintf0c2 libcroco3 libexpat1 libffi5
+ libgettextpo0 libglib2.0-0 libmagic1 libncursesw5 libpcre3 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python python-minimal python2.7 python2.7-minimal quilt
+ zlib1g-dev
+0 upgraded, 33 newly installed, 0 to remove and 46 not upgraded.
+Need to get 16.1 MB of archives.
+After this operation, 46.3 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libncursesw5 sparc 5.9-10 [119 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.2-1 [36.2 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libssl1.0.0 sparc 1.0.1c-4 [1077 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-9 [26.5 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.31-1 [252 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main libsqlite3-0 sparc 3.7.14.1-1 [426 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-6 [826 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.33.12+really2.32.4-3 [1645 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.6-1 [114 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libexpat1 sparc 2.1.0-1 [131 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-9 [129 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.3-1 [1033 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-9 [148 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main mime-support all 3.52-2 [35.2 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main python2.7-minimal sparc 2.7.3-5 [1606 kB]
+Get:22 http://debian.carnet.hr/debian/ unstable/main python2.7 sparc 2.7.3-5 [2607 kB]
+Get:23 http://debian.carnet.hr/debian/ unstable/main python-minimal all 2.7.3-3 [42.5 kB]
+Get:24 http://debian.carnet.hr/debian/ unstable/main python all 2.7.3-3 [179 kB]
+Get:25 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.118 [80.0 kB]
+Get:26 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:27 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-9 [1893 kB]
+Get:28 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:31 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
+Get:32 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 16.9 MB in 12s (1308 kB/s)
-Selecting previously unselected package libncursesw5.
-(Reading database ... 11074 files and directories currently installed.)
-Unpacking libncursesw5 (from .../libncursesw5_5.9-4_sparc.deb) ...
-Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_sparc.deb) ...
-Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_sparc.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.10-1_sparc.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_sparc.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_sparc.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_sparc.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.4-2_sparc.deb) ...
-Selecting previously unselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_sparc.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_sparc.deb) ...
-Selecting previously unselected package libdb4.8.
-Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_sparc.deb) ...
+Fetched 16.1 MB in 13s (1212 kB/s)
+Selecting previously unselected package libncursesw5:sparc.
+(Reading database ... 11087 files and directories currently installed.)
+Unpacking libncursesw5:sparc (from .../libncursesw5_5.9-10_sparc.deb) ...
+Selecting previously unselected package libpipeline1:sparc.
+Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.2-1_sparc.deb) ...
+Selecting previously unselected package libssl1.0.0:sparc.
+Unpacking libssl1.0.0:sparc (from .../libssl1.0.0_1.0.1c-4_sparc.deb) ...
+Selecting previously unselected package libasprintf0c2:sparc.
+Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-9_sparc.deb) ...
+Selecting previously unselected package libmagic1:sparc.
+Unpacking libmagic1:sparc (from .../libmagic1_5.11-2_sparc.deb) ...
+Selecting previously unselected package libpcre3:sparc.
+Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.31-1_sparc.deb) ...
+Selecting previously unselected package libsqlite3-0:sparc.
+Unpacking libsqlite3-0:sparc (from .../libsqlite3-0_3.7.14.1-1_sparc.deb) ...
+Selecting previously unselected package libxml2:sparc.
+Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-6_sparc.deb) ...
+Selecting previously unselected package libffi5:sparc.
+Unpacking libffi5:sparc (from .../libffi5_3.0.10-3_sparc.deb) ...
+Selecting previously unselected package libglib2.0-0:sparc.
+Unpacking libglib2.0-0:sparc (from .../libglib2.0-0_2.33.12+really2.32.4-3_sparc.deb) ...
+Selecting previously unselected package libcroco3:sparc.
+Unpacking libcroco3:sparc (from .../libcroco3_0.6.6-1_sparc.deb) ...
+Selecting previously unselected package libexpat1:sparc.
+Unpacking libexpat1:sparc (from .../libexpat1_2.1.0-1_sparc.deb) ...
+Selecting previously unselected package libunistring0:sparc.
+Unpacking libunistring0:sparc (from .../libunistring0_0.9.3-5_sparc.deb) ...
+Selecting previously unselected package libgettextpo0:sparc.
+Unpacking libgettextpo0:sparc (from .../libgettextpo0_0.18.1.1-9_sparc.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_sparc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_sparc.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-9_sparc.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.1-1_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.3-1_sparc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.10-1_sparc.deb) ...
+Unpacking file (from .../archives/file_5.11-2_sparc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_sparc.deb) ...
-Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_sparc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_sparc.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-2_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_sparc.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-5_sparc.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_sparc.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3-5_sparc.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.3-3_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-10_all.deb) ...
+Unpacking python (from .../python_2.7.3-3_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.118_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_sparc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-9_sparc.deb) ...
Selecting previously unselected package intltool-debian.
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_9.20120312_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-2_sparc.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-3_sparc.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_sparc.deb) ...
-Setting up libncursesw5 (5.9-4) ...
-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 (2.30.2-6) ...
+Selecting previously unselected package zlib1g-dev:sparc.
+Unpacking zlib1g-dev:sparc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_sparc.deb) ...
+Setting up libncursesw5:sparc (5.9-10) ...
+Setting up libpipeline1:sparc (1.2.2-1) ...
+Setting up libssl1.0.0:sparc (1.0.1c-4) ...
+Setting up libasprintf0c2:sparc (0.18.1.1-9) ...
+Setting up libmagic1:sparc (5.11-2) ...
+Setting up libpcre3:sparc (1:8.31-1) ...
+Setting up libsqlite3-0:sparc (3.7.14.1-1) ...
+Setting up libxml2:sparc (2.8.0+dfsg1-6) ...
+Setting up libffi5:sparc (3.0.10-3) ...
+Setting up libglib2.0-0:sparc (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-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 bsdmainutils (9.0.1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.1-1) ...
+Setting up libcroco3:sparc (0.6.6-1) ...
+Setting up libexpat1:sparc (2.1.0-1) ...
+Setting up libunistring0:sparc (0.9.3-5) ...
+Setting up libgettextpo0:sparc (0.18.1.1-9) ...
+Setting up bsdmainutils (9.0.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-1) ...
Building database of manual pages ...
-Setting up file (5.10-1) ...
-Setting up gettext-base (0.18.1.1-5) ...
-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 (2.7.3~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 file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-9) ...
+Setting up mime-support (3.52-2) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
+Setting up python2.7-minimal (2.7.3-5) ...
+Setting up python2.7 (2.7.3-5) ...
+Setting up python-minimal (2.7.3-3) ...
+Setting up python (2.7.3-3) ...
+Setting up cdbs (0.4.118) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120312) ...
-Setting up diffstat (1.55-2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
+Setting up zlib1g-dev:sparc (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.22-5 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_3.2.6-1
-Package versions: apt_0.8.15.9 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 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 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 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_1.4.12-3 gpgv_1.4.12-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 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 libc6-dev-sparc64_2.13-27 libc6-sparc64_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 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 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 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_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2+Debian29 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 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
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.118 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libc6-dev-sparc64_2.13-35 libc6-sparc64_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsqlite3-0_3.7.14.1-1 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-6 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-1 mawk_1.3.3-17 mime-support_3.52-2 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3-3 python-minimal_2.7.3-3 python2.7_2.7.3-5 python2.7-minimal_2.7.3-5 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,12 +338,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Mar 16 11:42:52 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Nov 4 09:07:58 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.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: warning: failed to verify signature on ./bedtools_2.17.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.17.0
+dpkg-source: info: unpacking bedtools_2.17.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.17.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -359,18 +354,18 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.16.1-1
- dpkg-source --before-build bedtools-2.16.1
+dpkg-buildpackage: source version 2.17.0-1
+ dpkg-source --before-build bedtools-2.17.0
dpkg-buildpackage: host architecture sparc
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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
* Cleaning-up BamTools API
* Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
dh_clean
rm -f debian/bedtools.substvars
rm -f debian/bedtools.*.debhelper
@@ -386,11 +381,11 @@ dh_clean
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -398,30 +393,32 @@ Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
-/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 `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
Building BEDTools:
=========================================================
-DETECTED_VERSION = v2.16.1
-CURRENT_VERSION = v2.16.1
+DETECTED_VERSION = v2.17.0
+CURRENT_VERSION =
+Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
@@ -432,7 +429,7 @@ CURRENT_VERSION = v2.16.1
- 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.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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
@@ -507,7 +504,7 @@ Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconv
- 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]
+genomeFile.cpp:60:26: 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**)':
@@ -516,7 +513,7 @@ annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunuse
- 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]
+bamToBed.cpp:85:10: 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**)':
@@ -566,10 +563,13 @@ getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+groupBy.cpp:82:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
+- Building in src/jaccard
+ * compiling jaccardMain.cpp
+ * compiling jaccard.cpp
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
@@ -592,6 +592,7 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
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]
+multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- Building in src/multiIntersectBed
* compiling multiIntersectBedMain.cpp
@@ -635,7 +636,7 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
- 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]
+subtractMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- Building in src/tagBam
* compiling tagBamMain.cpp
@@ -659,7 +660,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+make[1]: Leaving directory `/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -673,6 +674,7 @@ 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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -746,16 +748,38 @@ dh_install -pbedtools
cp -a ./bin/windowMaker debian/bedtools/usr/bin/
install -d debian/bedtools/usr/share/bedtools
cp -a ./genomes debian/bedtools/usr/share/bedtools/
+ install -d debian/bedtools/usr/share/bedtools/test
+ cp -a ./test/bamtobed debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/bed12tobed6 debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/closest debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/cluster debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/coverage debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/expand debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/flank debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/general debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/genomecov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/getfasta debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/groupBy debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/intersect debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/jaccard debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/map debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/merge debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/multicov debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/slop debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/subtract debian/bedtools/usr/share/bedtools/test/
+ cp -a ./test/test.sh debian/bedtools/usr/share/bedtools/test/
+ install -d debian/bedtools/etc/bash_completion.d
+ cp -a ./debian/bash_completion/bedtools debian/bedtools/etc/bash_completion.d/
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
+dh_compress -pbedtools -X test
cd debian/bedtools
- chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
- cd '/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+ 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 '/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0'
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
@@ -771,77 +795,85 @@ dh_fixperms -pbedtools
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 /build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+rm /build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ/bedtools-2.17.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
+ find debian/bedtools/etc -type f -printf '/etc/%P
+' >> debian/bedtools/DEBIAN/conffiles
+ chmod 644 debian/bedtools/DEBIAN/conffiles
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
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
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
+ (cd debian/bedtools >/dev/null ; find . -type f ! -path "./etc/bash_completion.d/bedtools" ! -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 -Z xz --build debian/bedtools ..
-dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bedtools_2.16.1-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.17.0-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.17.0-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.16.1
+ dpkg-source --after-build bedtools-2.17.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120316-1340
+Build finished at 20121104-1145
-bedtools_2.16.1-1_sparc.changes:
+bedtools_2.17.0-1_sparc.changes:
Format: 1.8
-Date: Fri, 16 Mar 2012 19:06:49 +0900
+Date: Sun, 04 Nov 2012 17:59:41 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.16.1-1
+Version: 2.17.0-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
+Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.16.1-1) unstable; urgency=low
+ bedtools (2.17.0-1) unstable; urgency=low
.
- b7f2405 New upstream release.
- 4add346 Corrected, updated and normalised Debian copyright.
- 00b426d Conforms to Debian Policy 3.9.3.
- 72c3c94 Verbose Debhelper.
+ bb9012e Imported Upstream version 2.16.2.
+ 9006b23 Imported Upstream version 2.17.0.
+ 9112569 Documented BEDTools license as a whole.
+ 325689c Removed Pre-Depends: dpkg (>= 1.15.6).
+ a781b14 Conforms with Policy 3.9.4.
+ 84b1167 Use Debhelper 9.
+ 0bf572d Distribute the test suite.
+ 422cd34 Bash completion for BEDTools.
Checksums-Sha1:
- 860dd1834056559f8993a4e9c507d71857a61984 372178 bedtools_2.16.1-1_sparc.deb
+ 0ebb1cd31d27bb537fb322fa210d3743118cca2c 388546 bedtools_2.17.0-1_sparc.deb
Checksums-Sha256:
- ca34bfe51acdb131f200eb0d7e822f8aa2afb5b3607fa88c753335d451c4a64b 372178 bedtools_2.16.1-1_sparc.deb
+ 841a99a125f1763646aed4f21cc66f6f98a3f8726abd1ef218801d8c9c5dff5c 388546 bedtools_2.17.0-1_sparc.deb
Files:
- 36b9be3f55c5e6063ec38575a9ea028b 372178 science optional bedtools_2.16.1-1_sparc.deb
+ 54f29f6973c28597c047f1336ff7e795 388546 science optional bedtools_2.17.0-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.16.1-1_sparc.deb
+bedtools_2.17.0-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 372178 bytes: control archive= 1974 bytes.
- 865 bytes, 19 lines control
- 2506 bytes, 44 lines md5sums
+ size 388546 bytes: control archive= 4109 bytes.
+ 32 bytes, 1 lines conffiles
+ 833 bytes, 18 lines control
+ 9605 bytes, 132 lines md5sums
Package: bedtools
- Version: 2.16.1-1
+ Version: 2.17.0-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1441
- Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 1606
+ Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -855,58 +887,168 @@ bedtools_2.16.1-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/bin/
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/bamToBed
--rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/expandCols
--rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/closestBed
--rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/complementBed
--rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/randomBed
--rwxr-xr-x root/root 36 2012-03-16 13:40 ./usr/bin/windowMaker
--rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/flankBed
--rwxr-xr-x root/root 36 2012-03-16 13:40 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/linksBed
--rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/coverageBed
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/bedToBam
--rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/windowBed
--rwxr-xr-x root/root 1413812 2012-03-16 13:40 ./usr/bin/bedtools
--rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/getOverlap
--rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/pairToBed
--rwxr-xr-x root/root 29 2012-03-16 13:40 ./usr/bin/sortBed
--rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/tagBam
--rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/mergeBed
--rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/intersectBed
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/annotateBed
--rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/subtractBed
--rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/clusterBed
--rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/nucBed
--rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/bamToFastq
--rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/mapBed
--rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/pairToPair
--rwxr-xr-x root/root 29 2012-03-16 13:40 ./usr/bin/slopBed
--rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/bedpeToBam
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2012-03-16 13:28 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/bin/
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 44 2012-11-04 11:45 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 42 2012-11-04 11:45 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 43 2012-11-04 11:45 ./usr/bin/complementBed
+-rwxr-xr-x root/root 1438428 2012-11-04 11:45 ./usr/bin/bedtools
+-rwxr-xr-x root/root 40 2012-11-04 11:45 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 43 2012-11-04 11:45 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 36 2012-11-04 11:45 ./usr/bin/tagBam
+-rwxr-xr-x root/root 36 2012-11-04 11:45 ./usr/bin/mapBed
+-rwxr-xr-x root/root 39 2012-11-04 11:45 ./usr/bin/randomBed
+-rwxr-xr-x root/root 36 2012-11-04 11:45 ./usr/bin/nucBed
+-rwxr-xr-x root/root 39 2012-11-04 11:45 ./usr/bin/windowBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 42 2012-11-04 11:45 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 43 2012-11-04 11:45 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 42 2012-11-04 11:45 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 42 2012-11-04 11:45 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 37 2012-11-04 11:45 ./usr/bin/slopBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 43 2012-11-04 11:45 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 40 2012-11-04 11:45 ./usr/bin/closestBed
+-rwxr-xr-x root/root 38 2012-11-04 11:45 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 36 2012-11-04 11:45 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 42 2012-11-04 11:45 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 44 2012-11-04 11:45 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 40 2012-11-04 11:45 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 40 2012-11-04 11:45 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 38 2012-11-04 11:45 ./usr/bin/linksBed
+-rwxr-xr-x root/root 43 2012-11-04 11:45 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 37 2012-11-04 11:45 ./usr/bin/sortBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 39 2012-11-04 11:45 ./usr/bin/expandCols
+-rwxr-xr-x root/root 38 2012-11-04 11:45 ./usr/bin/flankBed
+-rwxr-xr-x root/root 41 2012-11-04 11:45 ./usr/bin/bedToBam
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/share/
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-11-03 17:11 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-11-03 17:11 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/share/bedtools/test/
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/cluster/
+-rw-r--r-- root/root 264 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/in.bed
+-rw-r--r-- root/root 1455 2012-11-03 17:11 ./usr/share/bedtools/test/cluster/test-cluster.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/map/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/map/ivls.bed
+-rw-r--r-- root/root 186 2012-11-03 17:11 ./usr/share/bedtools/test/map/values2.bed
+-rw-r--r-- root/root 227 2012-11-03 17:11 ./usr/share/bedtools/test/map/values3.bed
+-rw-r--r-- root/root 2753 2012-11-03 17:11 ./usr/share/bedtools/test/map/test-map.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/map/values.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/groupBy/
+-rw-r--r-- root/root 885 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/test-groupby.sh
+-rw-r--r-- root/root 250 2012-11-03 17:11 ./usr/share/bedtools/test/groupBy/values3.header.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/merge/
+-rw-r--r-- root/root 57 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.names.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.bed
+-rw-r--r-- root/root 3642 2012-11-03 17:11 ./usr/share/bedtools/test/merge/test-merge.sh
+-rw-r--r-- root/root 147 2012-11-03 17:11 ./usr/share/bedtools/test/merge/a.full.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/closest/
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/b-one-bp-closer.bed
+-rw-r--r-- root/root 35 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.names.bed
+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/closest/a.bed
+-rw-r--r-- root/root 2126 2012-11-03 17:11 ./usr/share/bedtools/test/closest/test-closest.sh
+-rw-r--r-- root/root 1243 2012-11-03 17:11 ./usr/share/bedtools/test/test.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/intersect/
+-rw-r--r-- root/root 255 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/mapped_and_unmapped.sam
+-rw-r--r-- root/root 76 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/b.bed
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_nomatch.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match.bed
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/one_block.sam
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/a.bed
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks.sam
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/c.bed
+-rw-r--r-- root/root 10172 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/test-intersect.sh
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/intersect/three_blocks_match_1bp.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/slop/
+-rw-r--r-- root/root 3603 2012-11-03 17:11 ./usr/share/bedtools/test/slop/test-slop.sh
+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/slop/a.bed
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/slop/tiny.genome
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/genomecov/
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_nomatch.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match.bed
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/one_block.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks.sam
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/sam-w-del.sam
+-rw-r--r-- root/root 3402 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/test-genomecov.sh
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/genomecov/three_blocks_match_1bp.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/general/
+-rw-r--r-- root/root 1950 2012-11-03 17:11 ./usr/share/bedtools/test/general/test-general.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/expand/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/expand/expand.txt
+-rw-r--r-- root/root 1278 2012-11-03 17:11 ./usr/share/bedtools/test/expand/test-expand.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/multicov/
+-rw-r--r-- root/root 72 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/multicov.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.sam
+-rw-r--r-- root/root 3836 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/test-multicov.sh
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/one_block.bam.bai
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/multicov/two_blocks.sam
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+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_nomatch.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match.bed
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.bam.bai
+-rw-r--r-- root/root 156 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.sam
+-rw-r--r-- root/root 171 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.bam.bai
+-rw-r--r-- root/root 142 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/sam-w-del.sam
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/one_block.bam.bai
+-rw-r--r-- root/root 96 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks.bam.bai
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/two_blocks.sam
+-rw-r--r-- root/root 63 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/three_blocks_match_1bp.bed
+-rw-r--r-- root/root 988 2012-11-03 17:11 ./usr/share/bedtools/test/coverage/test-coverage.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bamtobed/
+-rw-r--r-- root/root 162 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/one_block.sam
+-rw-r--r-- root/root 176 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/three_blocks.sam
+-rw-r--r-- root/root 167 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/two_blocks.sam
+-rw-r--r-- root/root 3304 2012-11-03 17:11 ./usr/share/bedtools/test/bamtobed/test-bamtobed.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/getfasta/
+-rw-r--r-- root/root 61 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa
+-rw-r--r-- root/root 16 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.fa.fai
+-rw-r--r-- root/root 117 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/blocks.bed
+-rw-r--r-- root/root 1193 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/test-getfasta.sh
+-rw-r--r-- root/root 0 2012-11-03 17:11 ./usr/share/bedtools/test/getfasta/t.bed
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+-rw-r--r-- root/root 41 2012-11-03 17:11 ./usr/share/bedtools/test/flank/a.bed
+-rw-r--r-- root/root 10 2012-11-03 17:11 ./usr/share/bedtools/test/flank/tiny.genome
+-rw-r--r-- root/root 3859 2012-11-03 17:11 ./usr/share/bedtools/test/flank/test-flank.sh
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/subtract/
+-rw-r--r-- root/root 2532 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/test-subtract.sh
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/b.bed
+-rw-r--r-- root/root 36 2012-11-03 17:11 ./usr/share/bedtools/test/subtract/a.bed
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+-rw-r--r-- root/root 11 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/d.bed
+-rw-r--r-- root/root 77 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/b.bed
+-rw-r--r-- root/root 38 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/a.bed
+-rw-r--r-- root/root 825 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/test-jaccard.sh
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/jaccard/c.bed
+drwxr-xr-x root/root 0 2012-11-04 11:32 ./usr/share/bedtools/test/bed12tobed6/
+-rw-r--r-- root/root 52 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/two_blocks.bed
+-rw-r--r-- root/root 46 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/one_blocks.bed
+-rw-r--r-- root/root 60 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/three_blocks.bed
+-rw-r--r-- root/root 1919 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
+-rw-r--r-- root/root 18 2012-11-03 17:11 ./usr/share/bedtools/test/bed12tobed6/bed6.bed
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-11-03 17:11 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 5395 2012-11-04 05:11 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-11-03 17:11 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1089 2012-11-04 08:59 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./etc/
+drwxr-xr-x root/root 0 2012-11-04 11:45 ./etc/bash_completion.d/
+-rw-r--r-- root/root 638 2012-11-04 08:54 ./etc/bash_completion.d/bedtools
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -920,7 +1062,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-a73b8fd2-7abf-4eca-8927-aaae67d24e71/build/buildd-bedtools_2.16.1-1-sparc-nx_0id
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-936afc54-d88b-49fe-83e1-167f20c992d8/build/buildd-bedtools_2.17.0-1-sparc-Xb2QVZ
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -928,18 +1070,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 81448
-Build-Time: 741
+Build-Space: 84092
+Build-Time: 764
Distribution: sid
-Install-Time: 90
-Job: bedtools_2.16.1-1
+Install-Time: 105
+Job: bedtools_2.17.0-1
Package: bedtools
-Package-Time: 891
-Source-Version: 2.16.1-1
-Space: 81448
+Package-Time: 952
+Source-Version: 2.17.0-1
+Space: 84092
Status: successful
-Version: 2.16.1-1
+Version: 2.17.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120316-1340
-Build needed 00:14:51, 81448k disc space
-Signature with key '24E4F805' requested:
+Finished at 20121104-1145
+Build needed 00:15:52, 84092k disc space
+Signature with key 'E1D842D6' requested:
--
Suite of utilities for comparing genomic features.
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