[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.12.0-1-3-gd4672d3
Charles Plessy
plessy at debian.org
Sat Sep 24 02:43:41 UTC 2011
The following commit has been merged in the meta branch:
commit 3b1cda80101b456469e69f29e75dcc9577e0f03e
Author: Charles Plessy <plessy at debian.org>
Date: Sat Sep 24 11:35:56 2011 +0900
Collected build logs for version 2.1.13-1.
diff --git a/armel.log b/armel.log
index c11f3c2..6a0c6c5 100644
--- a/armel.log
+++ b/armel.log
@@ -1,67 +1,67 @@
-From buildd at ancina.debian.org Wed Jun 08 11:58:26 2011
-Return-path: <buildd at ancina.debian.org>
+From buildd at alain.debian.org Sun Sep 11 01:33:58 2011
+Return-path: <buildd at alain.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 ancina.debian.org>)
- id 1QUHOz-0006po-VH
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:58:26 +0000
-Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
+ (Exim 4.72) (envelope-from <buildd at alain.debian.org>)
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+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:33:58 +0000
+Received: from alain.islands.arm.com ([217.140.96.58] helo=alain.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
+ CN=alain.debian.org, EMAIL=hostmaster at alain.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1QUHOy-0003Se-Lp
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-Received: from buildd by ancina.debian.org with local (Exim 4.69)
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-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Wed, 8 Jun 2011 11:58:17 +0000
-From: Build Daemon <buildd at ancina.debian.org>
-To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on armel (dist=sid)
-Key-Id: A1EAA0BB
-Message-Id: <E1QUHOs-00089q-2W at ancina.debian.org>
+ (Exim 4.72) (envelope-from <buildd at alain.debian.org>)
+ id 1R2Yvk-00006S-T8
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:33:57 +0000
+Received: from buildd by alain.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alain.debian.org>)
+ id 1R2Yvj-0002pv-Mf; Sun, 11 Sep 2011 01:33:55 +0000
+Date: Sun, 11 Sep 2011 01:33:55 +0000
+Message-Id: <E1R2Yvj-0002pv-Mf at alain.debian.org>
+From: buildd on alain <buildd at alain.debian.org>
+To: buildd-porters at alain.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.1-1 on armel (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 ancina.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alain.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (armel) 08 Jun 2011 11:39 ║
+║ bedtools 2.13.1-1 (armel) 11 Sep 2011 01:07 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5755 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main 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/main armel Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Get:3 http://incoming.debian.org Sources [50.0 kB]
-Get:4 http://incoming.debian.org Packages [458 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5755 kB]
+Get:6 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:7 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:8 http://incoming.debian.org unstable/main armel Packages [7516 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [57.4 kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [102 kB]
+Get:11 http://ftp.uk.debian.org unstable/main armel Packages [7516 kB]
+Get:12 http://incoming.debian.org unstable/contrib armel Packages [55.6 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:13 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org Sources [32.0 kB]
+Get:16 http://incoming.debian.org Packages [290 kB]
+Get:17 http://ftp.uk.debian.org unstable/contrib armel Packages [55.6 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:18 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 510 kB in 10s (49.6 kB/s)
+Fetched 27.6 MB in 1min 2s (445 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 1s (644 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 1s (604 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,38 +120,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-5)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -160,38 +160,64 @@ 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 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
- procmail graphviz
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
+ www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev 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 groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 21 newly installed, 0 to remove and 6 not upgraded.
+Need to get 9375 kB of archives.
+After this operation, 28.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-3 [33.8 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.08-1 [245 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.08-1 [51.2 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-4 [139 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-4 [815 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.6-1 [1535 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-4 [409 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-4 [1984 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.54-1 [27.7 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 1 not upgraded.
-Need to get 0 B/8915 kB of archives.
-After this operation, 26.6 MB of additional disk space will be used.
+Fetched 9375 kB in 3s (3026 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10521 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
Selecting previously deselected package groff-base.
-(Reading database ... 11248 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_armel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_armel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_armel.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_armel.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_armel.deb) ...
+Unpacking file (from .../archives/file_5.08-1_armel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -201,39 +227,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_armel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_armel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up bsdmainutils (8.2.3) ...
+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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -241,11 +271,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.52.20110606-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-11 gcc-4.6_4.6.0-11 libc6-dev_2.13-5 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-11 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-11 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-11 gcc-4.6-base_4.6.0-11 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-5 libc-dev-bin_2.13-5 libc6_2.13-5 libc6-dev_2.13-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-11 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-11 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.4 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-2 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-3 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libudev0_170-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 nullmailer_1:1.05-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 wget_1.12-3.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32 armel (armv5tel)
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -255,14 +285,13 @@ Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -272,39 +301,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -313,36 +333,25 @@ No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
debian/rules build
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1/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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -356,9 +365,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -376,21 +382,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -403,7 +449,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -429,17 +475,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -450,11 +485,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -482,6 +512,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -494,9 +537,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -531,6 +574,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -545,19 +595,16 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-armel-diKF8g/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-armel-0nW2r_/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -592,85 +639,91 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/flankBed 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/unionBedGraphs 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/multiBamCov 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/bed12ToBed6 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/pairToBed 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/bamToBed 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/fastaFromBed 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/coverageBed 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/closestBed 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/overlap 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/closestBed 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/coverageBed 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/maskFastaFromBed 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/bedToBam 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/genomeCoverageBed 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/annotateBed 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/genomeCoverageBed 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/subtractBed 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/sortBed 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/cuffToTrans 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/pairToPair 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/shuffleBed 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/mergeBed 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/nucBed 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/bedToIgv 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/windowBed 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/fjoin 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/tagBam 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/linksBed 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/slopBed 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/intersectBed 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/slopBed 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/complementBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.12.0-1_armel.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (alain) <buildd_armel-alain at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1158
+Build finished at 20110911-0133
-bedtools_2.12.0-1_armel.changes:
+bedtools_2.13.1-1_armel.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
+Maintainer: armel Build Daemon (alain) <buildd_armel-alain at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 2b5a525b7acb98e8a6156ffc0ec4268999aca6f9 1434986 bedtools_2.12.0-1_armel.deb
+ 8f7899cfaceef6a77e022cebb051817bf0b6443f 519688 bedtools_2.13.1-1_armel.deb
Checksums-Sha256:
- ed65773182480cdce91aaf33e693841daf9e73d3c853284fb44e61fd87cf6bbe 1434986 bedtools_2.12.0-1_armel.deb
+ 2a7a2c93c9e4b28fc605fd9f24861924175e66aeb2de946b0bc6f67f7a330dd5 519688 bedtools_2.13.1-1_armel.deb
Files:
- 0b86bc52afa249351648c30b7fbe5f3a 1434986 science optional bedtools_2.12.0-1_armel.deb
+ 6b6c754a2d58890591556d039a80e7d1 519688 science optional bedtools_2.13.1-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_armel.deb
+bedtools_2.13.1-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 1434986 bytes: control archive= 1650 bytes.
- 761 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 519688 bytes: control archive= 1712 bytes.
+ 835 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3268
+ Installed-Size: 4052
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -680,49 +733,52 @@ bedtools_2.12.0-1_armel.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/bin/
--rwxr-xr-x root/root 112908 2011-06-08 11:57 ./usr/bin/bedToBam
--rwxr-xr-x root/root 219480 2011-06-08 11:57 ./usr/bin/pairToBed
--rwxr-xr-x root/root 102812 2011-06-08 11:57 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 121068 2011-06-08 11:57 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 94240 2011-06-08 11:57 ./usr/bin/mergeBed
--rwxr-xr-x root/root 75904 2011-06-08 11:57 ./usr/bin/overlap
--rwxr-xr-x root/root 94556 2011-06-08 11:57 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92308 2011-06-08 11:57 ./usr/bin/linksBed
--rwxr-xr-x root/root 108772 2011-06-08 11:57 ./usr/bin/closestBed
--rwxr-xr-x root/root 166188 2011-06-08 11:57 ./usr/bin/fjoin
--rwxr-xr-x root/root 126536 2011-06-08 11:57 ./usr/bin/sortBed
--rwxr-xr-x root/root 145676 2011-06-08 11:57 ./usr/bin/coverageBed
--rwxr-xr-x root/root 141956 2011-06-08 11:57 ./usr/bin/annotateBed
--rwxr-xr-x root/root 57116 2011-06-08 11:57 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 153880 2011-06-08 11:57 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 100856 2011-06-08 11:57 ./usr/bin/flankBed
--rwxr-xr-x root/root 90480 2011-06-08 11:57 ./usr/bin/complementBed
--rwxr-xr-x root/root 86576 2011-06-08 11:57 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 147880 2011-06-08 11:57 ./usr/bin/windowBed
--rwxr-xr-x root/root 162092 2011-06-08 11:57 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112816 2011-06-08 11:57 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 107184 2011-06-08 11:57 ./usr/bin/bamToBed
--rwxr-xr-x root/root 93876 2011-06-08 11:57 ./usr/bin/slopBed
--rwxr-xr-x root/root 160020 2011-06-08 11:57 ./usr/bin/pairToPair
--rwxr-xr-x root/root 121068 2011-06-08 11:57 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 104596 2011-06-08 11:57 ./usr/bin/subtractBed
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 11:40 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:57 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:32 ./
+drwxr-xr-x root/root 0 2011-09-11 01:33 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:33 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:33 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:10 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-09-11 01:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:33 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2011-09-11 01:33 ./usr/bin/
+-rwxr-xr-x root/root 240000 2011-09-11 01:33 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 105744 2011-09-11 01:33 ./usr/bin/closestBed
+-rwxr-xr-x root/root 227708 2011-09-11 01:33 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 302452 2011-09-11 01:33 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 122108 2011-09-11 01:33 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88188 2011-09-11 01:33 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 127480 2011-09-11 01:33 ./usr/bin/sortBed
+-rwxr-xr-x root/root 236596 2011-09-11 01:33 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 231828 2011-09-11 01:33 ./usr/bin/windowBed
+-rwxr-xr-x root/root 92280 2011-09-11 01:33 ./usr/bin/linksBed
+-rwxr-xr-x root/root 90512 2011-09-11 01:33 ./usr/bin/complementBed
+-rwxr-xr-x root/root 96420 2011-09-11 01:33 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 104564 2011-09-11 01:33 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 92272 2011-09-11 01:33 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 75900 2011-09-11 01:33 ./usr/bin/overlap
+-rwxr-xr-x root/root 93844 2011-09-11 01:33 ./usr/bin/slopBed
+-rwxr-xr-x root/root 186716 2011-09-11 01:33 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121748 2011-09-11 01:33 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 183404 2011-09-11 01:33 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 160184 2011-09-11 01:33 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 244128 2011-09-11 01:33 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 55428 2011-09-11 01:33 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 93844 2011-09-11 01:33 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 219548 2011-09-11 01:33 ./usr/bin/tagBam
+-rwxr-xr-x root/root 101260 2011-09-11 01:33 ./usr/bin/flankBed
+-rwxr-xr-x root/root 112816 2011-09-11 01:33 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 102796 2011-09-11 01:33 ./usr/bin/bedToIgv
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -736,68 +792,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-eaea20a9-e9db-4eac-950b-101c8263e8cc/build/buildd-bedtools_2.12.0-1-armel-diKF8g
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 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* libglib2.0-0* libmagic1*
- libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 1 not upgraded.
-After this operation, 26.6 MB disk space will be freed.
-(Reading database ... 12598 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 libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-armel-sbuild-f72ffd2e-57b3-438a-a585-cc5a0ec4836b/build/buildd-bedtools_2.13.1-1-armel-0nW2r_
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 73216
-Build-Time: 1059
+Build-Space: 95696
+Build-Time: 1371
Distribution: sid
-Install-Time: 33
-Job: bedtools_2.12.0-1
+Install-Time: 90
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 1125
-Source-Version: 2.12.0-1
-Space: 73216
+Package-Time: 1556
+Source-Version: 2.13.1-1
+Space: 95696
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1158
-Build needed 00:18:45, 73216k disc space
-Signature with key 'A1EAA0BB' requested:
+Finished at 20110911-0133
+Build needed 00:25:56, 95696k disc space
+Signature with key 'E7073AA3' requested:
+
diff --git a/hurd-i386.log b/hurd-i386.log
index c9b7a39..bc26bf1 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,65 +1,207 @@
-From buildd at rossini.debian.net Wed Jun 08 11:22:35 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+From buildd at mozart.debian.net Mon Sep 12 02:12:51 2011
+Return-path: <buildd at mozart.debian.net>
+Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1QUGqI-0001Wo-2Y
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:22:34 +0000
-Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
- by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1QUGqF-000Cne-VG; Wed, 08 Jun 2011 13:22:32 +0200
-Received: from buildd by rossini.debian.net with local (Exim 4.72)
- (envelope-from <buildd at rossini.debian.net>)
- id 1QUGqG-0001BU-I8; Wed, 08 Jun 2011 11:22:32 +0000
-Date: Wed, 08 Jun 2011 11:22:32 +0000
-Message-Id: <E1QUGqG-0001BU-I8 at rossini.debian.net>
-From: Build Daemon <buildd at rossini.debian.net>
-To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at buildd.debian-ports.org,
+ (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
+ id 1R2w0w-0002cY-V2
+ for logs at buildd.debian.org; Mon, 12 Sep 2011 02:12:51 +0000
+Received: from mozart.debian.net ([10.1.0.1])
+ by callisto.debian.net with esmtp (Exim 4.69)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1R2w0p-0002Is-MN; Mon, 12 Sep 2011 03:12:43 +0100
+Received: from buildd by mozart.debian.net with local (Exim 4.76)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1R2w0o-0001IC-4x; Mon, 12 Sep 2011 02:12:43 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.78; A2.07; B3.08; Q3.08)
+Date: Mon, 12 Sep 2011 02:12:41 +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, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on hurd-i386 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+Subject: Log for successful build of bedtools_2.13.1-1 on hurd-i386 (dist=sid)
+Message-Id: <E1R2w0o-0001IC-4x at mozart.debian.net>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rossini.debian.net
+sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (hurd-i386) 08 Jun 2011 11:07 ║
+║ bedtools 2.13.1-1 (hurd-i386) 12 sept. 2011 01:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
+Distribution: sid
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y
-Start Time: 20110608-1107
-Ign file: ./ InRelease
-Ign file: ./ Release.gpg
-Ign file: ./ Release
-Ign file: ./ Translation-en
-Hit http://ftp.ch.debian.org unstable InRelease
-Hit http://ftp.ch.debian.org experimental InRelease
+
+I: NOTICE: Log filtering will replace 'build/bedtools-gkOcvg/bedtools-2.13.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bedtools-gkOcvg' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'home/buildd/build/chroot-sid' with '«CHROOT»'
+W: Stripped single quote from command for security:
+ use strict;
+ use warnings;
+ use POSIX;
+ use FileHandle;
+
+ my $lockfile="/var/lock/sbuild";
+ my $try = 0;
+
+ repeat:
+ if (!sysopen( F, $lockfile, O_WRONLY|O_CREAT|O_TRUNC|O_EXCL, 0644 )){
+ if ($! == EEXIST) {
+ # lock file exists, wait
+ goto repeat if !open( F, "<$lockfile" );
+ my $line = <F>;
+ my ($job, $pid, $user);
+ close( F );
+ if ($line !~ /^(\S+)\s+(\S+)\s+(\S+)/) {
+ print STDERR "Bad lock file contents ($lockfile) -- still trying\n";
+ } else {
+ ($job, $pid, $user) = ($1, $2, $3);
+ if (kill( 0, $pid ) == 0 && $! == ESRCH) {
+ # process doesn't exist anymore, remove stale lock
+ print STDERR "Removing stale lock file $lockfile ".
+ "(job $job, pid $pid, user $user)\n";
+ if (!unlink($lockfile)) {
+ if ($! != ENOENT) {
+ print STDERR "Cannot remove chroot lock file $lockfile: $!\n";
+ exit 1;
+ }
+ }
+ }
+ }
+ ++$try;
+ if ($try > 120) {
+ print STDERR "Lockfile $lockfile still present after " .
+ 120 * 5 . " seconds -- giving up\n";
+ exit 1;
+ }
+ print STDERR "Another sbuild process (job $job, pid $pid by user $user) is currently using the build chroot; waiting...\n"
+ if $try == 1;
+ sleep 5;
+ goto repeat;
+ } else {
+ print STDERR "Can't create lock file $lockfile: $!\n";
+ exit 1;
+ }
+ }
+
+ F->print("bedtools_2.13.1-1 1356 buildd\n");
+ F->close();
+
+ exit 0;
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
Ign http://incoming.debian.org InRelease
+Get:1 http://ftp.uk.debian.org sid InRelease [146 kB]
+Get:2 http://ftp.fr.debian.org sid InRelease [146 kB]
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1604 B]
Ign http://ftp.debian-ports.org unreleased InRelease
-Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.ch.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.ch.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.ch.debian.org unstable/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.ch.debian.org unstable/main TranslationIndex
-Hit http://ftp.ch.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.ch.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.ch.debian.org experimental/non-free Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [48.8 kB]
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:5 http://ftp.debian-ports.org unreleased Release.gpg [836 B]
+Get:6 http://ftp.debian-ports.org unreleased Release [25.8 kB]
+Get:7 http://ftp.fr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:8 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:9 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:10 http://ftp.fr.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:11 http://ftp.fr.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:12 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Get:13 http://ftp.uk.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:14 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Get:15 http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex [2023 B]
+Get:16 http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
+Get:17 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
+Get:18 http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex [2023 B]
+Get:19 http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
+Get:20 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
+Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
+Get:21 http://ftp.debian-ports.org unreleased/main hurd-i386 Packages [49.7 kB]
+Get:22 http://incoming.debian.org Sources [36.7 kB]
+Get:23 http://ftp.uk.debian.org sid/main 2011-09-10-2018.11.pdiff [14.8 kB]
+Get:24 http://ftp.uk.debian.org sid/contrib 2011-09-11-1413.17.pdiff [484 B]
+Get:25 http://ftp.uk.debian.org sid/non-free 2011-09-11-1413.17.pdiff [873 B]
+Get:26 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-10-2018.11.pdiff [5696 B]
+Get:27 http://ftp.uk.debian.org sid/contrib hurd-i386 2011-09-11-1413.17.pdiff [29 B]
+Get:28 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-09-11-1413.17.pdiff [848 B]
+Get:29 http://ftp.fr.debian.org sid/main 2011-09-10-2018.11.pdiff [14.8 kB]
+Get:30 http://ftp.fr.debian.org sid/contrib 2011-09-11-1413.17.pdiff [484 B]
+Get:31 http://ftp.fr.debian.org sid/non-free 2011-09-11-1413.17.pdiff [873 B]
+Get:32 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-10-2018.11.pdiff [5696 B]
+Get:33 http://ftp.uk.debian.org sid/main 2011-09-10-2018.11.pdiff [14.8 kB]
+Get:34 http://ftp.fr.debian.org sid/contrib hurd-i386 2011-09-11-1413.17.pdiff [29 B]
+Get:35 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-09-11-1413.17.pdiff [848 B]
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Get:4 http://incoming.debian.org Packages [468 kB]
+Get:36 http://incoming.debian.org Packages [233 kB]
+Ign http://ftp.uk.debian.org sid/contrib Translation-en
+Ign http://ftp.uk.debian.org sid/non-free Translation-en
+Ign http://ftp.fr.debian.org sid/contrib Translation-en
+Ign http://ftp.fr.debian.org sid/non-free Translation-en
Ign http://ftp.debian-ports.org unreleased/main Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 519 kB in 1min 39s (5232 B/s)
+Get:37 http://ftp.uk.debian.org sid/contrib 2011-09-11-1413.17.pdiff [484 B]
+Get:38 http://ftp.uk.debian.org sid/main 2011-09-11-0215.26.pdiff [9396 B]
+Get:39 http://ftp.uk.debian.org sid/non-free 2011-09-11-1413.17.pdiff [873 B]
+Get:40 http://ftp.uk.debian.org sid/contrib 2011-09-11-2015.34.pdiff [29 B]
+Get:41 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-10-2018.11.pdiff [5696 B]
+Get:42 http://ftp.uk.debian.org sid/non-free 2011-09-11-2015.34.pdiff [351 B]
+Get:43 http://ftp.uk.debian.org sid/contrib hurd-i386 2011-09-11-1413.17.pdiff [29 B]
+Get:44 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-0215.26.pdiff [5403 B]
+Get:45 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-09-11-1413.17.pdiff [848 B]
+Get:46 http://ftp.fr.debian.org sid/main 2011-09-10-2018.11.pdiff [14.8 kB]
+Get:47 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-09-11-2015.34.pdiff [254 B]
+Get:48 http://ftp.fr.debian.org sid/contrib 2011-09-11-1413.17.pdiff [484 B]
+Get:49 http://ftp.fr.debian.org sid/main 2011-09-11-0215.26.pdiff [9396 B]
+Get:50 http://ftp.fr.debian.org sid/non-free 2011-09-11-1413.17.pdiff [873 B]
+Get:51 http://ftp.fr.debian.org sid/contrib 2011-09-11-2015.34.pdiff [29 B]
+Get:52 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-10-2018.11.pdiff [5696 B]
+Get:53 http://ftp.fr.debian.org sid/non-free 2011-09-11-2015.34.pdiff [351 B]
+Get:54 http://ftp.fr.debian.org sid/contrib hurd-i386 2011-09-11-1413.17.pdiff [29 B]
+Get:55 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-0215.26.pdiff [5403 B]
+Get:56 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-09-11-1413.17.pdiff [848 B]
+Get:57 http://ftp.uk.debian.org sid/main 2011-09-11-0215.26.pdiff [9396 B]
+Get:58 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-09-11-2015.34.pdiff [254 B]
+Get:59 http://ftp.uk.debian.org sid/contrib 2011-09-11-2015.34.pdiff [29 B]
+Get:60 http://ftp.uk.debian.org sid/main 2011-09-11-0816.36.pdiff [2437 B]
+Get:61 http://ftp.uk.debian.org sid/non-free 2011-09-11-2015.34.pdiff [351 B]
+Get:62 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-0215.26.pdiff [5403 B]
+Get:63 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-09-11-2015.34.pdiff [254 B]
+Get:64 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-0816.36.pdiff [1206 B]
+Get:65 http://ftp.fr.debian.org sid/main 2011-09-11-0215.26.pdiff [9396 B]
+Get:66 http://ftp.fr.debian.org sid/contrib 2011-09-11-2015.34.pdiff [29 B]
+Get:67 http://ftp.fr.debian.org sid/main 2011-09-11-0816.36.pdiff [2437 B]
+Get:68 http://ftp.fr.debian.org sid/non-free 2011-09-11-2015.34.pdiff [351 B]
+Get:69 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-0215.26.pdiff [5403 B]
+Get:70 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-09-11-2015.34.pdiff [254 B]
+Get:71 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-0816.36.pdiff [1206 B]
+Get:72 http://ftp.uk.debian.org sid/main 2011-09-11-0816.36.pdiff [2437 B]
+Get:73 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-0816.36.pdiff [1206 B]
+Get:74 http://ftp.uk.debian.org sid/main 2011-09-11-1413.17.pdiff [14.7 kB]
+Get:75 http://ftp.fr.debian.org sid/main 2011-09-11-0816.36.pdiff [2437 B]
+Get:76 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-1413.17.pdiff [10.8 kB]
+Get:77 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-0816.36.pdiff [1206 B]
+Get:78 http://ftp.fr.debian.org sid/main 2011-09-11-1413.17.pdiff [14.7 kB]
+Get:79 http://ftp.uk.debian.org sid/main 2011-09-11-1413.17.pdiff [14.7 kB]
+Get:80 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-1413.17.pdiff [10.8 kB]
+Get:81 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-1413.17.pdiff [10.8 kB]
+Get:82 http://ftp.uk.debian.org sid/main 2011-09-11-2015.34.pdiff [10.6 kB]
+Get:83 http://ftp.fr.debian.org sid/main 2011-09-11-1413.17.pdiff [14.7 kB]
+Get:84 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-2015.34.pdiff [2454 B]
+Get:85 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-1413.17.pdiff [10.8 kB]
+Get:86 http://ftp.fr.debian.org sid/main 2011-09-11-2015.34.pdiff [10.6 kB]
+Get:87 http://ftp.uk.debian.org sid/main 2011-09-11-2015.34.pdiff [10.6 kB]
+Get:88 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-2015.34.pdiff [2454 B]
+Get:89 http://ftp.uk.debian.org sid/main hurd-i386 2011-09-11-2015.34.pdiff [2454 B]
+Get:90 http://ftp.fr.debian.org sid/main 2011-09-11-2015.34.pdiff [10.6 kB]
+Get:91 http://ftp.fr.debian.org sid/main hurd-i386 2011-09-11-2015.34.pdiff [2454 B]
+Fetched 829 kB in 6min 9s (2246 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,117 +222,105 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 6s (124 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://ftp.uk.debian.org/debian/ sid/main bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://ftp.uk.debian.org/debian/ sid/main bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://ftp.uk.debian.org/debian/ sid/main bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 0s (684 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-yBnYA2/apt_archive/sbuild-build-depends-core-dummy.deb'.
+gpg: WARNING: using insecure memory!
+gpg: please see http://www.gnupg.org/faq.html for more information
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-cdbs: missing
-debhelper: missing
-Using default version 8.1.6
-quilt: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libboost-iostreams1.42.0
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/716 B of archives.
+After this operation, 0 B of additional disk space will be used.
+WARNING: The following packages cannot be authenticated!
+ sbuild-build-depends-core-dummy
+Authentication warning overridden.
+Selecting previously deselected package sbuild-build-depends-core-dummy.
+(Reading database ... 13789 files and directories currently installed.)
+Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, 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, zlib1g-dev
+Filtered 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, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
+dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-RiWMjn/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
+gpg: WARNING: using insecure memory!
+gpg: please see http://www.gnupg.org/faq.html for more information
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libexpat1 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
+ cdbs diffstat quilt zlib1g-dev
Suggested packages:
- devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ devscripts procmail graphviz
Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libexpat1 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
- quilt zlib1g-dev
-0 upgraded, 17 newly installed, 0 to remove and 18 not upgraded.
-Need to get 0 B/7142 kB of archives.
-After this operation, 21.9 MB of additional disk space will be used.
+ cdbs diffstat quilt sbuild-build-depends-bedtools-dummy zlib1g-dev
+0 upgraded, 5 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/645 kB of archives.
+After this operation, 1786 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
- libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
- diffstat quilt zlib1g-dev
+ cdbs diffstat quilt zlib1g-dev sbuild-build-depends-bedtools-dummy
Authentication warning overridden.
-Selecting previously deselected package libmagic1.
-(Reading database ... 13452 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_hurd-i386.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_hurd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_hurd-i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+(Reading database ... 13789 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
+Selecting previously deselected package sbuild-build-depends-bedtools-dummy.
+Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
-Setting up libmagic1 (5.03-5+b1) ...
-Setting up file (5.03-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.13-4 dpkg-dev_1.16.0.3 hurd-dev_20110519-1 gnumach-dev_2:1.3.99.dfsg.git20110305-1 gcc-4.6_4.6.0-9 g++-4.6_4.6.0-9 binutils_2.21.51.20110523-1 libstdc++6-4.6-dev_4.6.0-9 libstdc++6_4.6.0-9
-Package versions: adduser_3.112+nmu2 apt_0.8.14.1 apt-utils_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.51.20110523-1 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20110421 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.4_4.4.5-10 cpp-4.5_4.5.3-1 cpp-4.6_4.6.0-9 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.6-2 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-10 g++-4.5_4.5.3-1 g++-4.6_4.6.0-9 gcc_4:4.4.5-7 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5_4.5.3-1 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-9 gcc-4.6-base_4.6.0-9 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran-4.4_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20110305-1 gnupg_1.4.11-3 gnupg-curl_1.4.11-3 gobjc-4.4_4.4.5-10 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-1 hurd-dev_20110519-1 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.44-3 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4+b2 libboost-iostreams1.46.1_1.46.1-5 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc0.3_2.13-4 libc0.3-dev_2.13-4 libc0.3-xen_2.13-4 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.6-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.6.0-9 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.6.0-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.6.0-9 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncursesw5_5.9-1 libnewt0.52_0.52.11-2 libobjc2_4.5.3-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.3-1 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.2.0-2 libpng12-0_1.2.44-2 libpopt0_1.16-1 libppl-c2_0.10.2-9 libppl-c4_0.11.2-3 libppl7_0.10.2-9 libppl9_0.11.2-3 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libpwl5_0.11.2-3 libquadmath0_4.6.0-9 libreadline6_6.2-2 librtmp0_2.3-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-2 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-2 libslang2_2.2.4-2 libss2_1.41.12-4 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-9 libstdc++6-4.4-dev_4.4.5-10 libstdc++6-4.5-dev_4.5.3-1 libstdc++6-4.6-dev_4.6.0-9 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-14+hurd.2 libxdmcp-dev_1:1.1.0-1 libxdmcp6_1:1.1.0-1 libxml2_2.7.8.dfsg-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 netcat-traditional_1.10-39 openssl_1.0.0d-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-2 tzdata_2011g-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 x11proto-core-dev_7.0.21-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.0.3 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-18 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-119 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-10 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_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc0.3_2.13-18 libc0.3-dev_2.13-18 libc0.3-xen_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.10-1 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-0.3 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libobjc2_4.5.3-8 libp11-kit0_0.4-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-4 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-7 random-egd_0.5-0+hurd.1 readline-common_6.2-4 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -200,19 +330,44 @@ Package versions: adduser_3.112+nmu2 apt_0.8.14.1 apt-utils_0.8.14.1 base-files_
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
+FAKEROOTEGID=0
+FAKEROOTEUID=0
+FAKEROOTFGID=0
+FAKEROOTFUID=0
+FAKEROOTGID=0
+FAKEROOTSGID=0
+FAKEROOTSUID=0
+FAKEROOTUID=0
+HOME=/home/buildd
+LOGNAME=buildd
+OLDPWD=/
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin
+PWD=/«PKGBUILDDIR»
+SHELL=/bin/sh
+SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env'
+SUDO_GID=105
+SUDO_UID=60000
+SUDO_USER=buildd
+TERM=linux
+USER=buildd
+USERNAME=root
dpkg-buildpackage
─────────────────
@@ -223,50 +378,51 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Entering directory `/«PKGBUILDDIR»'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
No patches applied
rm -rf ./.pc
- debian/rules build
rm -f debian/stamp-patch*
+ debian/rules build
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS 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_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+cd . && QUILT_PATCHES=/«PKGBUILDDIR»/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_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Entering directory `/«PKGBUILDDIR»'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -280,11 +436,10 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
+genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+genomeFile.cpp:51:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- Building in src/utils/gzstream
g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
@@ -298,24 +453,74 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
+annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
- Building in src/bamToBed
* compiling bamToBed.cpp
+bamToBed.cpp: In function 'int main(int, char**)':
+bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
* linking bamToBed
- Building in src/bedToBam
* compiling bedToBam.cpp
+bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -341,13 +546,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -358,11 +556,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -385,21 +578,49 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/mergeBed
* compiling mergeMain.cpp
+mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
+overlap.cpp: In function 'int main(int, char**)':
+overlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
* compiling overlap.cpp
* linking overlap
- Building in src/pairToBed
+pairToBedMain.cpp: In function 'int 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:254:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
* linking pairToBed
- Building in src/pairToPair
+pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToPairMain.cpp
* compiling pairToPair.cpp
+pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
+pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
+pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
* linking pairToPair
- Building in src/shuffleBed
@@ -418,13 +639,26 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* linking sortBed
- Building in src/subtractBed
+subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractMain.cpp
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBamMain.cpp
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
+unionBedGraphsMain.cpp: In function 'int 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]
* linking unionBedGraphs
- Building in src/windowBed
@@ -432,7 +666,7 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y/bedtools-2.12.0'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -441,6 +675,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -475,59 +710,76 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../bedtools_2.12.0-1_hurd-i386.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1122
+Build finished at 20110912-0211
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+bedtools_2.13.1-1_hurd-i386.changes:
+────────────────────────────────────
-bedtools_2.12.0-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 7ff42ec7138f5b41d0052cd861b750eaf209c267 1413172 bedtools_2.12.0-1_hurd-i386.deb
+ ce4c62644466d17c65032c4b077a5924203670f6 659216 bedtools_2.13.1-1_hurd-i386.deb
Checksums-Sha256:
- 0876ac512bf01a4dabb4beb5967c4b80b4eb05bb05f0578e6c0afdc3bcd7674e 1413172 bedtools_2.12.0-1_hurd-i386.deb
+ 6c04ed10968c5113d6064f61fe0582bbece3df0fefefbbb07f5f7daf55bb5a18 659216 bedtools_2.13.1-1_hurd-i386.deb
Files:
- eaab6c2cc574668dc31c66a8760fdcc7 1413172 science optional bedtools_2.12.0-1_hurd-i386.deb
+ 2f42dff3773f55609a98eb704f3f877f 659216 science optional bedtools_2.13.1-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_hurd-i386.deb
+bedtools_2.13.1-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 1413172 bytes: control archive= 1662 bytes.
- 766 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 659216 bytes: control archive= 1727 bytes.
+ 841 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3252
- Depends: libc0.3 (>= 2.13), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4744
+ Depends: libc0.3 (>= 2.2.6), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -537,88 +789,108 @@ bedtools_2.12.0-1_hurd-i386.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-12 02:01 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-09-12 02:09 ./usr/bin/
+-rwxr-xr-x root/root 102688 2011-09-12 02:09 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 220432 2011-09-12 02:09 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96344 2011-09-12 02:09 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227616 2011-09-12 02:09 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 120944 2011-09-12 02:09 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 120904 2011-09-12 02:09 ./usr/bin/closestBed
+-rwxr-xr-x root/root 104548 2011-09-12 02:09 ./usr/bin/complementBed
+-rwxr-xr-x root/root 280908 2011-09-12 02:09 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 141760 2011-09-12 02:09 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 112732 2011-09-12 02:09 ./usr/bin/flankBed
+-rwxr-xr-x root/root 293892 2011-09-12 02:09 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 301404 2011-09-12 02:09 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105120 2011-09-12 02:09 ./usr/bin/linksBed
+-rwxr-xr-x root/root 108872 2011-09-12 02:09 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 106432 2011-09-12 02:09 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297300 2011-09-12 02:09 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 141808 2011-09-12 02:09 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88152 2011-09-12 02:09 ./usr/bin/overlap
+-rwxr-xr-x root/root 366956 2011-09-12 02:09 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178272 2011-09-12 02:09 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129148 2011-09-12 02:09 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 104540 2011-09-12 02:09 ./usr/bin/slopBed
+-rwxr-xr-x root/root 142248 2011-09-12 02:09 ./usr/bin/sortBed
+-rwxr-xr-x root/root 112704 2011-09-12 02:09 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 268776 2011-09-12 02:09 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59508 2011-09-12 02:09 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285012 2011-09-12 02:09 ./usr/bin/windowBed
-drwxr-xr-x root/root 0 2011-06-08 11:19 ./
-drwxr-xr-x root/root 0 2011-06-08 11:19 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:20 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:20 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-06-08 11:20 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 11:10 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-08 11:20 ./usr/bin/
--rwxr-xr-x root/root 154992 2011-06-08 11:20 ./usr/bin/annotateBed
--rwxr-xr-x root/root 92944 2011-06-08 11:20 ./usr/bin/bamToBed
--rwxr-xr-x root/root 85044 2011-06-08 11:20 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 116936 2011-06-08 11:20 ./usr/bin/bedToBam
--rwxr-xr-x root/root 104552 2011-06-08 11:20 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 100452 2011-06-08 11:20 ./usr/bin/closestBed
--rwxr-xr-x root/root 97724 2011-06-08 11:20 ./usr/bin/complementBed
--rwxr-xr-x root/root 157912 2011-06-08 11:20 ./usr/bin/coverageBed
--rwxr-xr-x root/root 125116 2011-06-08 11:20 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 125116 2011-06-08 11:20 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 174308 2011-06-08 11:20 ./usr/bin/fjoin
--rwxr-xr-x root/root 100540 2011-06-08 11:20 ./usr/bin/flankBed
--rwxr-xr-x root/root 174708 2011-06-08 11:20 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 174308 2011-06-08 11:20 ./usr/bin/intersectBed
--rwxr-xr-x root/root 96356 2011-06-08 11:20 ./usr/bin/linksBed
--rwxr-xr-x root/root 96368 2011-06-08 11:20 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 100452 2011-06-08 11:20 ./usr/bin/mergeBed
--rwxr-xr-x root/root 88460 2011-06-08 11:20 ./usr/bin/overlap
--rwxr-xr-x root/root 190712 2011-06-08 11:20 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121644 2011-06-08 11:20 ./usr/bin/pairToPair
--rwxr-xr-x root/root 109516 2011-06-08 11:20 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 97716 2011-06-08 11:20 ./usr/bin/slopBed
--rwxr-xr-x root/root 101040 2011-06-08 11:20 ./usr/bin/sortBed
--rwxr-xr-x root/root 92260 2011-06-08 11:20 ./usr/bin/subtractBed
--rwxr-xr-x root/root 60992 2011-06-08 11:20 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 163144 2011-06-08 11:20 ./usr/bin/windowBed
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
+│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.12.0-1-hurd-i386-W43v1Y
-(Reading database ... 14424 files and directories currently installed.)
-Removing zlib1g-dev ...
+Purging /«BUILDDIR»
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ cdbs* diffstat* quilt* sbuild-build-depends-bedtools-dummy*
+ sbuild-build-depends-core-dummy* zlib1g-dev*
+0 upgraded, 0 newly installed, 6 to remove and 1 not upgraded.
+After this operation, 1786 kB disk space will be freed.
+(Reading database ... 13959 files and directories currently installed.)
+Removing sbuild-build-depends-bedtools-dummy ...
Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
Removing quilt ...
Purging configuration files for quilt ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing file ...
-Purging configuration files for file ...
Removing diffstat ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
+Removing sbuild-build-depends-core-dummy ...
+Removing zlib1g-dev ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1122
-Build needed 00:14:54, 56880k disc space
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: hurd-i386
+Build-Space: 91708
+Build-Time: 586
+Distribution: sid
+Install-Time: 97
+Job: bedtools_2.13.1-1
+Package: bedtools
+Package-Time: 1099
+Source-Version: 2.13.1-1
+Space: 91708
+Status: successful
+Version: 2.13.1-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110912-0211
+Build needed 00:18:19, 91708k disc space
diff --git a/i386.log b/i386.log
index 3aa96f9..7d8df4f 100644
--- a/i386.log
+++ b/i386.log
@@ -1,67 +1,67 @@
-From buildd at murphy.debian.org Wed Jun 08 12:15:53 2011
+From buildd at murphy.debian.org Sun Sep 11 01:12:06 2011
Return-path: <buildd at murphy.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 murphy.debian.org>)
- id 1QUHft-0000YX-3c
- for logs at buildd.debian.org; Wed, 08 Jun 2011 12:15:53 +0000
+ id 1R2Yac-0005D3-L9
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:12:06 +0000
Received: from murphy.debian.org ([70.103.162.31])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=murphy.debian.org, EMAIL=hostmaster at murphy.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 murphy.debian.org>)
- id 1QUHfs-0002CN-3E
- for logs at buildd.debian.org; Wed, 08 Jun 2011 12:15:52 +0000
+ id 1R2Yab-0007i1-0g
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:12:05 +0000
Received: from buildd by murphy.debian.org with local (Exim 4.72)
(envelope-from <buildd at murphy.debian.org>)
- id 1QUHfq-0001hr-BT; Wed, 08 Jun 2011 12:15:50 +0000
-Message-Id: <E1QUHfq-0001hr-BT at murphy.debian.org>
+ id 1R2YaZ-0006rE-9b; Sun, 11 Sep 2011 01:12:03 +0000
+Message-Id: <E1R2YaZ-0006rE-9b 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: Wed, 8 Jun 2011 12:15:50 +0000
+Date: Sun, 11 Sep 2011 01:12:03 +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_2.12.0-1 on i386 (dist=sid)
-Key-Id: 1C3F1E5E
+Subject: Log for successful build of bedtools_2.13.1-1 on i386 (dist=sid)
+Key-Id: AC7BC9C1
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (i386) 08 Jun 2011 12:12 ║
+║ bedtools 2.13.1-1 (i386) 11 Sep 2011 01:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: i386
+Hit http://ftp.us.debian.org sid InRelease
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
+Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
Get:1 http://incoming.debian.org Release.gpg [836 B]
Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.us.debian.org sid InRelease
+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
+Ign http://ftp.us.debian.org sid/contrib TranslationIndex
+Hit http://ftp.us.debian.org sid/main TranslationIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/main i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
-Get:3 http://incoming.debian.org Sources [49.9 kB]
-Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
-Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
-Ign http://ftp.us.debian.org sid/contrib TranslationIndex
-Hit http://ftp.us.debian.org sid/main TranslationIndex
-Get:4 http://incoming.debian.org Packages [473 kB]
+Get:3 http://incoming.debian.org Sources [32.0 kB]
Ign http://ftp.us.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Packages [290 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 525 kB in 4s (115 kB/s)
+Fetched 325 kB in 5s (61.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 2s (323 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 2s (327 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,38 +120,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-5)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-20)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -174,28 +174,28 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 3 not upgraded.
-Need to get 0 B/9487 kB of archives.
-After this operation, 28.3 MB of additional disk space will be used.
+0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/9553 kB of archives.
+After this operation, 28.8 MB of additional disk space will be used.
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10794 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10855 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_i386.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_i386.deb) ...
+Unpacking file (from .../archives/file_5.08-1_i386.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -205,43 +205,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -249,11 +249,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
-Toolchain package versions: binutils_2.21.52.20110606-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-11 gcc-4.6_4.6.0-11 libc6-dev_2.13-5 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-11 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-11 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.6_4.6.0-11 gcc-4.6-base_4.6.0-11 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-5 libc-dev-bin_2.13-5 libc6_2.13-5 libc6-dev_2.13-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-11 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-11 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-11 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,12 +264,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -285,24 +285,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -313,22 +313,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1/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_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -342,9 +343,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -362,21 +360,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -389,7 +427,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -415,17 +453,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -436,11 +463,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -468,6 +490,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -480,9 +515,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -517,6 +552,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -531,7 +573,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-i386-nhfdke/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -540,6 +582,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -574,59 +617,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.12.0-1_i386.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1215
+Build finished at 20110911-0111
-bedtools_2.12.0-1_i386.changes:
+bedtools_2.13.1-1_i386.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
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
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 6315facc69b47d23b0221f3cd3629dbf5315533e 1615774 bedtools_2.12.0-1_i386.deb
+ 447b7e9472158fb5c4dd7c3dfe9ca575c43adc39 659932 bedtools_2.13.1-1_i386.deb
Checksums-Sha256:
- 4de8206917bc8706a2304dc3fd39d1dceeb67489449f032660e841424d202648 1615774 bedtools_2.12.0-1_i386.deb
+ c11c0899e857a75183621caaad88cf75bc81c2c991658d3e1d5d8b2931faa3d6 659932 bedtools_2.13.1-1_i386.deb
Files:
- 68d0fd75888ab4a4da48b81c0ebfc17c 1615774 science optional bedtools_2.12.0-1_i386.deb
+ 4fd0df79e608d8b655ca636ffcb68cbc 659932 science optional bedtools_2.13.1-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_i386.deb
+bedtools_2.13.1-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 1615774 bytes: control archive= 1651 bytes.
- 761 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 659932 bytes: control archive= 1715 bytes.
+ 836 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3712
- Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4736
+ Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -636,49 +684,52 @@ bedtools_2.12.0-1_i386.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/bin/
--rwxr-xr-x root/root 121144 2011-06-08 12:15 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 184216 2011-06-08 12:15 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 96344 2011-06-08 12:15 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 143692 2011-06-08 12:15 ./usr/bin/sortBed
--rwxr-xr-x root/root 174288 2011-06-08 12:15 ./usr/bin/windowBed
--rwxr-xr-x root/root 120928 2011-06-08 12:15 ./usr/bin/closestBed
--rwxr-xr-x root/root 171260 2011-06-08 12:15 ./usr/bin/coverageBed
--rwxr-xr-x root/root 108664 2011-06-08 12:15 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 166108 2011-06-08 12:15 ./usr/bin/annotateBed
--rwxr-xr-x root/root 141500 2011-06-08 12:15 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 141500 2011-06-08 12:15 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 129276 2011-06-08 12:15 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 252384 2011-06-08 12:15 ./usr/bin/pairToBed
--rwxr-xr-x root/root 108640 2011-06-08 12:15 ./usr/bin/mergeBed
--rwxr-xr-x root/root 105324 2011-06-08 12:15 ./usr/bin/complementBed
--rwxr-xr-x root/root 88152 2011-06-08 12:15 ./usr/bin/overlap
--rwxr-xr-x root/root 176576 2011-06-08 12:15 ./usr/bin/pairToPair
--rwxr-xr-x root/root 106372 2011-06-08 12:15 ./usr/bin/linksBed
--rwxr-xr-x root/root 113488 2011-06-08 12:15 ./usr/bin/subtractBed
--rwxr-xr-x root/root 196936 2011-06-08 12:15 ./usr/bin/fjoin
--rwxr-xr-x root/root 130940 2011-06-08 12:15 ./usr/bin/bedToBam
--rwxr-xr-x root/root 63600 2011-06-08 12:15 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 118492 2011-06-08 12:15 ./usr/bin/bamToBed
--rwxr-xr-x root/root 113896 2011-06-08 12:15 ./usr/bin/flankBed
--rwxr-xr-x root/root 190692 2011-06-08 12:15 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105036 2011-06-08 12:15 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 12:12 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 12:15 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/bin/
+-rwxr-xr-x root/root 120944 2011-09-11 01:11 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 293764 2011-09-11 01:11 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 268648 2011-09-11 01:11 ./usr/bin/tagBam
+-rwxr-xr-x root/root 96344 2011-09-11 01:11 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 141584 2011-09-11 01:11 ./usr/bin/nucBed
+-rwxr-xr-x root/root 141992 2011-09-11 01:11 ./usr/bin/sortBed
+-rwxr-xr-x root/root 281928 2011-09-11 01:11 ./usr/bin/windowBed
+-rwxr-xr-x root/root 119364 2011-09-11 01:11 ./usr/bin/closestBed
+-rwxr-xr-x root/root 280908 2011-09-11 01:11 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 108744 2011-09-11 01:11 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 102400 2011-09-11 01:11 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 141536 2011-09-11 01:11 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 129148 2011-09-11 01:11 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 366956 2011-09-11 01:11 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 106304 2011-09-11 01:11 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 104548 2011-09-11 01:11 ./usr/bin/complementBed
+-rwxr-xr-x root/root 297300 2011-09-11 01:11 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 88152 2011-09-11 01:11 ./usr/bin/overlap
+-rwxr-xr-x root/root 178272 2011-09-11 01:11 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 104896 2011-09-11 01:11 ./usr/bin/linksBed
+-rwxr-xr-x root/root 112704 2011-09-11 01:11 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 227616 2011-09-11 01:11 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 59508 2011-09-11 01:11 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 220336 2011-09-11 01:11 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 112732 2011-09-11 01:11 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301404 2011-09-11 01:11 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 104540 2011-09-11 01:11 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:08 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -692,11 +743,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-5b04930d-997f-4435-9442-a0f07b8f6bc8/build/buildd-bedtools_2.12.0-1-i386-CoZuzJ
+Purging /var/lib/schroot/mount/sid-i386-sbuild-6fadc8c4-276d-40b9-b68b-e3d99ad53b7f/build/buildd-bedtools_2.13.1-1-i386-nhfdke
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -705,9 +756,9 @@ The following packages will be REMOVED:
groff-base* html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 3 not upgraded.
-After this operation, 28.3 MB disk space will be freed.
-(Reading database ... 12328 files and directories currently installed.)
+0 upgraded, 0 newly installed, 21 to remove and 0 not upgraded.
+After this operation, 28.8 MB disk space will be freed.
+(Reading database ... 12265 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing man-db ...
@@ -747,18 +798,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 71128
-Build-Time: 171
+Build-Space: 91692
+Build-Time: 194
Distribution: sid
Install-Time: 10
-Job: bedtools_2.12.0-1
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 192
-Source-Version: 2.12.0-1
-Space: 71128
+Package-Time: 216
+Source-Version: 2.13.1-1
+Space: 91692
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1215
-Build needed 00:03:12, 71128k disc space
-Signature with key '1C3F1E5E' requested:
+Finished at 20110911-0111
+Build needed 00:03:36, 91692k disc space
+Signature with key 'AC7BC9C1' requested:
diff --git a/ia64.log b/ia64.log
index 08b456f..74d1d62 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,65 +1,66 @@
-From buildd at caballero.debian.org Wed Jun 08 16:06:29 2011
-Return-path: <buildd at caballero.debian.org>
+From buildd at mundy.debian.org Sun Sep 11 01:23:48 2011
+Return-path: <buildd at mundy.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 caballero.debian.org>)
- id 1QULH2-00024d-LA
- for logs at buildd.debian.org; Wed, 08 Jun 2011 16:06:29 +0000
-Received: from caballero.debian.org ([193.201.200.200])
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1R2Ylv-0006x1-Dl
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:23:48 +0000
+Received: from mundy.debian.org ([192.25.206.62])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=caballero.debian.org,
- EMAIL=hostmaster at caballero.debian.org (verified)
+ CN=mundy.debian.org, EMAIL=hostmaster at mundy.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 1QULGy-0001jR-RA; Wed, 08 Jun 2011 16:06:25 +0000
-Received: from buildd by caballero.debian.org with local (Exim 4.69)
- (envelope-from <buildd at caballero.debian.org>) id 1QULGx-00071L-MG
- for buildd-porters at caballero.debian.org; Wed, 08 Jun 2011 16:06:23 +0000
-From: buildd on caballero <buildd at caballero.debian.org>
-To: buildd-porters at caballero.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on ia64 (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1R2Ylo-00088C-8p; Sun, 11 Sep 2011 01:23:40 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1R2Yll-0008OB-SZ; Sun, 11 Sep 2011 01:23:37 +0000
+Date: Sun, 11 Sep 2011 01:23:37 +0000
+Message-Id: <E1R2Yll-0008OB-SZ at mundy.debian.org>
+From: buildd on mundy <buildd at mundy.debian.org>
+To: dannf at master.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.1-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QULGx-00071L-MG at caballero.debian.org>
-Date: Wed, 08 Jun 2011 16:06:23 +0000
-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 caballero.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (ia64) 08 Jun 2011 16:01 ║
+║ bedtools 2.13.1-1 (ia64) 11 Sep 2011 01:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: ia64
-Hit http://mirror.positive-internet.com sid InRelease
-Hit http://mirror.positive-internet.com sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://spohr.debian.org unstable InRelease [146 kB]
+Get:2 http://spohr.debian.org unstable/main Sources [5755 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [57.4 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [102 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [7416 kB]
Ign http://incoming.debian.org InRelease
-Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
-Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
-Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
-Ign http://mirror.positive-internet.com sid/contrib TranslationIndex
-Hit http://mirror.positive-internet.com sid/main TranslationIndex
-Hit http://incoming.debian.org Release.gpg
-Ign http://mirror.positive-internet.com sid/contrib 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/main ia64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5755 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [56.3 kB]
+Ign http://spohr.debian.org unstable/contrib TranslationIndex
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://spohr.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7416 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [56.3 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [32.0 kB]
+Get:18 http://incoming.debian.org Packages [290 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
+Fetched 27.4 MB in 17s (1598 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,11 +81,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/debian/ sid/main bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/debian/ sid/main bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/debian/ sid/main bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 1s (610 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 0s (677 kB/s)
Download complete and in download only mode
Check arch
@@ -98,18 +99,24 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 22 not upgraded.
+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 6 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+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 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -118,38 +125,38 @@ Checking correctness of dependencies...
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, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6.1-dev: already installed (2.13-4)
-gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6.1-dev: already installed (2.13-19)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -157,6 +164,9 @@ Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
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 libglib2.0-0 libmagic1 libpcre3 libpipeline1
@@ -171,29 +181,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 21 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.4 MB of archives.
+After this operation, 43.3 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
+Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
+Get:3 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.08-1 [272 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main file ia64 5.08-1 [54.0 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-4 [173 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-4 [1177 kB]
+Get:10 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.6-1 [1973 kB]
+Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
+Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-4 [467 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-4 [2441 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
+Get:20 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:21 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 22 not upgraded.
-Need to get 0 B/11.5 MB of archives.
-After this operation, 39.9 MB of additional disk space will be used.
+Fetched 11.4 MB in 0s (13.0 MB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10607 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10487 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_ia64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_ia64.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_ia64.deb) ...
+Unpacking file (from .../archives/file_5.08-1_ia64.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_ia64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -203,43 +235,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_ia64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -247,11 +279,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+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 6 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.51.20110523-1 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6.1-dev_2.13-4 libstdc++6_4.6.0-11 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.38-5
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110523-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-11 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6.1_2.13-4 libc6.1-dev_2.13-4 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-11 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-11 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-2 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-11 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6.1-dev_2.13-19 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-19 libc-dev-bin_2.13-19 libc6.1_2.13-19 libc6.1-dev_2.13-19 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-19 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -261,14 +296,13 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -278,39 +312,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -319,36 +344,25 @@ No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
debian/rules build
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1/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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -362,11 +376,10 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
+genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+genomeFile.cpp:51:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- Building in src/utils/gzstream
g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
@@ -380,24 +393,74 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
+annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
- Building in src/bamToBed
* compiling bamToBed.cpp
+bamToBed.cpp: In function 'int main(int, char**)':
+bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
* linking bamToBed
- Building in src/bedToBam
* compiling bedToBam.cpp
+bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -423,13 +486,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -440,11 +496,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -467,21 +518,49 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/mergeBed
* compiling mergeMain.cpp
+mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
+overlap.cpp: In function 'int main(int, char**)':
+overlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
* linking overlap
- Building in src/pairToBed
* compiling pairToBedMain.cpp
+pairToBedMain.cpp: In function 'int main(int, char**)':
+pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
+pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
+pairToBed.cpp:254:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
+pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToPair.cpp
+pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
+pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
+pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
* linking pairToPair
- Building in src/shuffleBed
@@ -501,12 +580,25 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/subtractBed
* compiling subtractMain.cpp
+subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
+unionBedGraphsMain.cpp: In function 'int 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]
* linking unionBedGraphs
- Building in src/windowBed
@@ -514,19 +606,16 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -559,62 +648,67 @@ dh_makeshlibs -pbedtools
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
-dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/bedtools/usr/bin/flankBed debian/bedtools/usr/bin/unionBedGraphs debian/bedtools/usr/bin/pairToBed debian/bedtools/usr/bin/bed12ToBed6 debian/bedtools/usr/bin/bamToBed debian/bedtools/usr/bin/overlap debian/bedtools/usr/bin/fastaFromBed debian/bedtools/usr/bin/closestBed debian/bedtools/usr/bin/coverageBed debian/bedtools/usr/bin/maskFastaFromBed debian/bedtools/usr/bin/bedToBam debian/bedtools/usr/bin/genomeCoverageBed debian/bedtools/usr/bin/annotateBed debian/bedtools/usr/bin/subtractBed debian/bedtools/usr/bin/sortBed debian/bedtools/usr/bin/cuffToTrans debian/bedtools/usr/bin/pairToPair debian/bedtools/usr/bin/shuffleBed debian/bedtools/usr/bin/mergeBed debian/bedtools/usr/bin/bedToIgv debian/bedtools/usr/bin/windowBed debian/bedtools/usr/bin/fjoin debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed" were not uselessly linked against it (they use none of its symbols).
+dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/bedtools/usr/bin/flankBed debian/bedtools/usr/bin/unionBedGraphs debian/bedtools/usr/bin/multiBamCov debian/bedtools/usr/bin/pairToBed debian/bedtools/usr/bin/bed12ToBed6 debian/bedtools/usr/bin/bamToBed debian/bedtools/usr/bin/coverageBed debian/bedtools/usr/bin/closestBed debian/bedtools/usr/bin/fastaFromBed debian/bedtools/usr/bin/overlap debian/bedtools/usr/bin/maskFastaFromBed debian/bedtools/usr/bin/bedToBam debian/bedtools/usr/bin/genomeCoverageBed debian/bedtools/usr/bin/annotateBed debian/bedtools/usr/bin/subtractBed debian/bedtools/usr/bin/sortBed debian/bedtools/usr/bin/pairToPair debian/bedtools/usr/bin/shuffleBed debian/bedtools/usr/bin/mergeBed debian/bedtools/usr/bin/nucBed debian/bedtools/usr/bin/bedToIgv debian/bedtools/usr/bin/windowBed debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/tagBam debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed" were not uselessly linked against it (they use none of its symbols).
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../bedtools_2.12.0-1_ia64.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1606
+Build finished at 20110911-0123
-bedtools_2.12.0-1_ia64.changes:
+bedtools_2.13.1-1_ia64.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
+Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 76cb7b80dbadfe77cee87f5c04432846375bd7c9 2106114 bedtools_2.12.0-1_ia64.deb
+ fdb16f89167d253b61d819a3f1d6f909f2881c00 720166 bedtools_2.13.1-1_ia64.deb
Checksums-Sha256:
- 32d93ebbe64f4365c78bb30626f73487b9060cd7ef04591df4864186969dfc7c 2106114 bedtools_2.12.0-1_ia64.deb
+ 4980390175f4d313dd7485ca2f0c5db70ecc8b2140033aab8b9eb19cbd4af03c 720166 bedtools_2.13.1-1_ia64.deb
Files:
- 01fce0f7072c450390fa4c29f9057f0e 2106114 science optional bedtools_2.12.0-1_ia64.deb
+ dea4aa02818809c0187560d85ea630ee 720166 science optional bedtools_2.13.1-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_ia64.deb
+bedtools_2.13.1-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 2106114 bytes: control archive= 1664 bytes.
- 774 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 720166 bytes: control archive= 1730 bytes.
+ 848 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 6744
+ Installed-Size: 9580
Depends: libc6.1 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -624,49 +718,52 @@ bedtools_2.12.0-1_ia64.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 16:01 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-08 16:05 ./usr/bin/
--rwxr-xr-x root/root 335296 2011-06-08 16:05 ./usr/bin/annotateBed
--rwxr-xr-x root/root 201528 2011-06-08 16:05 ./usr/bin/bamToBed
--rwxr-xr-x root/root 183424 2011-06-08 16:05 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 249536 2011-06-08 16:05 ./usr/bin/bedToBam
--rwxr-xr-x root/root 222800 2011-06-08 16:05 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 213472 2011-06-08 16:05 ./usr/bin/closestBed
--rwxr-xr-x root/root 213040 2011-06-08 16:05 ./usr/bin/complementBed
--rwxr-xr-x root/root 336184 2011-06-08 16:05 ./usr/bin/coverageBed
--rwxr-xr-x root/root 269472 2011-06-08 16:05 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 269472 2011-06-08 16:05 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 369832 2011-06-08 16:05 ./usr/bin/fjoin
--rwxr-xr-x root/root 213936 2011-06-08 16:05 ./usr/bin/flankBed
--rwxr-xr-x root/root 373048 2011-06-08 16:05 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 368392 2011-06-08 16:05 ./usr/bin/intersectBed
--rwxr-xr-x root/root 205384 2011-06-08 16:05 ./usr/bin/linksBed
--rwxr-xr-x root/root 206552 2011-06-08 16:05 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 223584 2011-06-08 16:05 ./usr/bin/mergeBed
--rwxr-xr-x root/root 192208 2011-06-08 16:05 ./usr/bin/overlap
--rwxr-xr-x root/root 405504 2011-06-08 16:05 ./usr/bin/pairToBed
--rwxr-xr-x root/root 266072 2011-06-08 16:05 ./usr/bin/pairToPair
--rwxr-xr-x root/root 235424 2011-06-08 16:05 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 208192 2011-06-08 16:05 ./usr/bin/slopBed
--rwxr-xr-x root/root 225320 2011-06-08 16:05 ./usr/bin/sortBed
--rwxr-xr-x root/root 197528 2011-06-08 16:05 ./usr/bin/subtractBed
--rwxr-xr-x root/root 129808 2011-06-08 16:05 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 350496 2011-06-08 16:05 ./usr/bin/windowBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:15 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/bin/
+-rwxr-xr-x root/root 456592 2011-09-11 01:23 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 178016 2011-09-11 01:23 ./usr/bin/overlap
+-rwxr-xr-x root/root 267936 2011-09-11 01:23 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 469176 2011-09-11 01:23 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 217248 2011-09-11 01:23 ./usr/bin/complementBed
+-rwxr-xr-x root/root 586280 2011-09-11 01:23 ./usr/bin/windowBed
+-rwxr-xr-x root/root 214384 2011-09-11 01:23 ./usr/bin/slopBed
+-rwxr-xr-x root/root 304704 2011-09-11 01:23 ./usr/bin/sortBed
+-rwxr-xr-x root/root 225672 2011-09-11 01:23 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 296840 2011-09-11 01:23 ./usr/bin/nucBed
+-rwxr-xr-x root/root 293040 2011-09-11 01:23 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 220408 2011-09-11 01:23 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 233320 2011-09-11 01:23 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 247728 2011-09-11 01:23 ./usr/bin/closestBed
+-rwxr-xr-x root/root 621632 2011-09-11 01:23 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 198832 2011-09-11 01:23 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 558992 2011-09-11 01:23 ./usr/bin/tagBam
+-rwxr-xr-x root/root 244240 2011-09-11 01:23 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 219672 2011-09-11 01:23 ./usr/bin/linksBed
+-rwxr-xr-x root/root 215952 2011-09-11 01:23 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 572584 2011-09-11 01:23 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 379184 2011-09-11 01:23 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 602928 2011-09-11 01:23 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 619648 2011-09-11 01:23 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 118456 2011-09-11 01:23 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 769440 2011-09-11 01:23 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 231104 2011-09-11 01:23 ./usr/bin/flankBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -680,73 +777,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-14c4dfce-4ef8-4e62-9142-ce5f3132fd14/build/buildd-bedtools_2.12.0-1-ia64-dMxw7B
-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* libcroco3* libglib2.0-0* libmagic1*
- libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 22 not upgraded.
-After this operation, 39.9 MB disk space will be freed.
-(Reading database ... 11960 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing 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 libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-4ddb4911-b790-4238-a222-048556b6ed53/build/buildd-bedtools_2.13.1-1-ia64-ftwQbc
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 81372
-Build-Time: 273
+Build-Space: 151388
+Build-Time: 512
Distribution: sid
-Install-Time: 22
-Job: bedtools_2.12.0-1
+Install-Time: 60
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 306
-Source-Version: 2.12.0-1
-Space: 81372
+Package-Time: 624
+Source-Version: 2.13.1-1
+Space: 151388
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1606
-Build needed 00:05:06, 81372k disc space
+Finished at 20110911-0123
+Build needed 00:10:24, 151388k disc space
+Signature with key '96FA48F4' requested:
diff --git a/info b/info
index 3bd1cd7..85d58fb 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-kfreebsd-amd64~1307530892~sid~successful
-powerpc~1307530966~sid~successful
-kfreebsd-i386~1307531039~sid~successful
-hurd-i386~1307532155~sid~successful
-mips~1307533004~sid~successful
-armel~1307534306~sid~successful
-i386~1307535353~sid~successful
-mipsel~1307536157~sid~successful
-ia64~1307549193~sid~successful
-sparc~1307587156~sid~successful
-s390~1307658598~sid~successful
+i386~1315703527~sid~successful
+powerpc~1315703659~sid~successful
+kfreebsd-i386~1315703927~sid~successful
+s390~1315704226~sid~successful
+ia64~1315704228~sid~successful
+mips~1315704574~sid~successful
+mipsel~1315704673~sid~successful
+armel~1315704839~sid~successful
+kfreebsd-amd64~1315706138~sid~successful
+sparc~1315712893~sid~successful
+hurd-i386~1315793571~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index fc0809f..8611756 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,4 +1,4 @@
-From buildd at fano.debian.org Wed Jun 08 11:01:32 2011
+From buildd at fano.debian.org Sun Sep 11 01:55:37 2011
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,
@@ -6,43 +6,53 @@ 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 fano.debian.org>)
- id 1QUGVv-0007A2-UW
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:01:32 +0000
+ id 1R2ZGj-00040H-9G
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:55:37 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1QUGVu-0001n5-D7; Wed, 08 Jun 2011 11:01:30 +0000
+ id 1R2ZGh-00016a-JL; Sun, 11 Sep 2011 01:55:35 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1QUGVr-0009Dt-VQ; Wed, 08 Jun 2011 11:01:28 +0000
-Message-Id: <E1QUGVr-0009Dt-VQ at fano.debian.org>
+ id 1R2ZGe-000PkI-79; Sun, 11 Sep 2011 01:55:32 +0000
+Message-Id: <E1R2ZGe-000PkI-79 at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 8 Jun 2011 11:01:27 +0000
+Date: Sun, 11 Sep 2011 01:55:32 +0000
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.13.1-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 91116966
+Key-Id: 911EAB69
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (kfreebsd-amd64) 08 Jun 2011 10:57 ║
+║ bedtools 2.13.1-1 (kfreebsd-amd64) 11 Sep 2011 01:51 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: kfreebsd-amd64
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://mirror-ubc.debian.org sid InRelease
+Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
+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://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-amd64 Packages/DiffIndex
@@ -54,23 +64,14 @@ Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages
Ign http://mirror-ubc.debian.org sid/contrib Translation-en
Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
-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
+Get:2 http://incoming.debian.org Release [1604 B]
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:3 http://incoming.debian.org Sources [32.0 kB]
+Get:4 http://incoming.debian.org Packages [289 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
+Fetched 323 kB in 3s (87.7 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -91,11 +92,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 1s (483 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 1s (514 kB/s)
Download complete and in download only mode
Check arch
@@ -109,18 +110,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.17-1)
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 6 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 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -129,38 +130,38 @@ Checking correctness of dependencies...
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, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.1-4+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+freebsd-utils: already installed (8.2+ds2-5)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -183,26 +184,26 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/9591 kB of archives.
-After this operation, 26.8 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 6 not upgraded.
+Need to get 0 B/9581 kB of archives.
+After this operation, 27.2 MB of additional disk space will be used.
+Selecting previously deselected package libpipeline1.
+(Reading database ... 12210 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package groff-base.
-(Reading database ... 12251 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-amd64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_5.08-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -212,40 +213,40 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up groff-base (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -253,11 +254,11 @@ 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 6 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.52.20110606-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-11 gcc-4.6_4.6.0-11 kfreebsd-kernel-headers_0.54 libc0.1-dev_2.13-5 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-11 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-11 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-11 gcc-4.6-base_4.6.0-11 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.54 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-5 libc-dev-bin_2.13-5 libc0.1_2.13-5 libc0.1-dev_2.13-5 libcam0_8.2-1 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-11 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-11 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.2-2 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-2 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-11 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-2 libsbuf0_8.1-5 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 ufsutils_8.2-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-19 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.17-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-19 libc-dev-bin_2.13-19 libc0.1_2.13-19 libc0.1-dev_2.13-19 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-19 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -268,12 +269,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -289,24 +290,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -317,22 +318,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1/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_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -346,9 +348,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -366,21 +365,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -393,7 +432,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -419,17 +458,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -440,11 +468,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -472,6 +495,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -484,9 +520,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -521,6 +557,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -535,7 +578,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -544,6 +587,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -578,59 +622,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.12.0-1_kfreebsd-amd64.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1100
+Build finished at 20110911-0155
-bedtools_2.12.0-1_kfreebsd-amd64.changes:
+bedtools_2.13.1-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
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
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 2d86301e3e4bed648b1a29743976c294acc19134 1614762 bedtools_2.12.0-1_kfreebsd-amd64.deb
+ c048b7afe96c049cd0987f390cb6e1f10b5ef634 646470 bedtools_2.13.1-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 3c6caacf7abf6d37f7d2e29c4d50b0080db459c99c0d81b007a86bb82b2e639a 1614762 bedtools_2.12.0-1_kfreebsd-amd64.deb
+ 131f11d491a314dd656d1f60031abba8e9b8b7213f97ab7338afc0875de1ee86 646470 bedtools_2.13.1-1_kfreebsd-amd64.deb
Files:
- 0bfeb3ce4572c6b4c34a449d7162d395 1614762 science optional bedtools_2.12.0-1_kfreebsd-amd64.deb
+ 116dcef71188cea5fc1e8838ea1a528e 646470 science optional bedtools_2.13.1-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_kfreebsd-amd64.deb
+bedtools_2.13.1-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 1614762 bytes: control archive= 1656 bytes.
- 772 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 646470 bytes: control archive= 1730 bytes.
+ 846 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3730
+ Installed-Size: 4808
Depends: libc0.1 (>= 2.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -640,49 +689,52 @@ bedtools_2.12.0-1_kfreebsd-amd64.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 10:58 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/bin/
--rwxr-xr-x root/root 171728 2011-06-08 11:00 ./usr/bin/annotateBed
--rwxr-xr-x root/root 123088 2011-06-08 11:00 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101832 2011-06-08 11:00 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 138920 2011-06-08 11:00 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126456 2011-06-08 11:00 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126424 2011-06-08 11:00 ./usr/bin/closestBed
--rwxr-xr-x root/root 110816 2011-06-08 11:00 ./usr/bin/complementBed
--rwxr-xr-x root/root 175808 2011-06-08 11:00 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147088 2011-06-08 11:00 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 147088 2011-06-08 11:00 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 200416 2011-06-08 11:00 ./usr/bin/fjoin
--rwxr-xr-x root/root 118224 2011-06-08 11:00 ./usr/bin/flankBed
--rwxr-xr-x root/root 188128 2011-06-08 11:00 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 196320 2011-06-08 11:00 ./usr/bin/intersectBed
--rwxr-xr-x root/root 114160 2011-06-08 11:00 ./usr/bin/linksBed
--rwxr-xr-x root/root 114312 2011-06-08 11:00 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114136 2011-06-08 11:00 ./usr/bin/mergeBed
--rwxr-xr-x root/root 93640 2011-06-08 11:00 ./usr/bin/overlap
--rwxr-xr-x root/root 257792 2011-06-08 11:00 ./usr/bin/pairToBed
--rwxr-xr-x root/root 183800 2011-06-08 11:00 ./usr/bin/pairToPair
--rwxr-xr-x root/root 134680 2011-06-08 11:00 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110032 2011-06-08 11:00 ./usr/bin/slopBed
--rwxr-xr-x root/root 150976 2011-06-08 11:00 ./usr/bin/sortBed
--rwxr-xr-x root/root 118560 2011-06-08 11:00 ./usr/bin/subtractBed
--rwxr-xr-x root/root 69112 2011-06-08 11:00 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 175800 2011-06-08 11:00 ./usr/bin/windowBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:52 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-09-11 01:54 ./usr/bin/
+-rwxr-xr-x root/root 109976 2011-09-11 01:54 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 214848 2011-09-11 01:54 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101832 2011-09-11 01:54 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 226616 2011-09-11 01:54 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 126456 2011-09-11 01:54 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 126376 2011-09-11 01:54 ./usr/bin/closestBed
+-rwxr-xr-x root/root 110176 2011-09-11 01:54 ./usr/bin/complementBed
+-rwxr-xr-x root/root 272720 2011-09-11 01:54 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 147088 2011-09-11 01:54 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 118224 2011-09-11 01:54 ./usr/bin/flankBed
+-rwxr-xr-x root/root 290768 2011-09-11 01:54 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 294856 2011-09-11 01:54 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 110016 2011-09-11 01:54 ./usr/bin/linksBed
+-rwxr-xr-x root/root 115192 2011-09-11 01:54 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 114088 2011-09-11 01:54 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 291928 2011-09-11 01:54 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 147112 2011-09-11 01:54 ./usr/bin/nucBed
+-rwxr-xr-x root/root 93640 2011-09-11 01:54 ./usr/bin/overlap
+-rwxr-xr-x root/root 356328 2011-09-11 01:54 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 180224 2011-09-11 01:54 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 134672 2011-09-11 01:54 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 110032 2011-09-11 01:54 ./usr/bin/slopBed
+-rwxr-xr-x root/root 148040 2011-09-11 01:54 ./usr/bin/sortBed
+-rwxr-xr-x root/root 264496 2011-09-11 01:54 ./usr/bin/tagBam
+-rwxr-xr-x root/root 118168 2011-09-11 01:54 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 65024 2011-09-11 01:54 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 278456 2011-09-11 01:54 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -696,11 +748,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1307530651-33169/build/buildd-bedtools_2.12.0-1-kfreebsd-amd64-AKXwDc
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1315705886-96757/build/buildd-bedtools_2.13.1-1-kfreebsd-amd64-Km4gug
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 6 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -708,9 +760,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpcre3*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 10 not upgraded.
-After this operation, 26.8 MB disk space will be freed.
-(Reading database ... 13616 files and directories currently installed.)
+0 upgraded, 0 newly installed, 20 to remove and 6 not upgraded.
+After this operation, 27.2 MB disk space will be freed.
+(Reading database ... 13573 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -748,18 +800,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 103882
-Build-Time: 159
+Build-Space: 131776
+Build-Time: 172
Distribution: sid
Install-Time: 36
-Job: bedtools_2.12.0-1
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 208
-Source-Version: 2.12.0-1
-Space: 103882
+Package-Time: 223
+Source-Version: 2.13.1-1
+Space: 131776
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1100
-Build needed 00:03:28, 103882k disc space
-Signature with key '91116966' requested:
+Finished at 20110911-0155
+Build needed 00:03:43, 131776k disc space
+Signature with key '911EAB69' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index b07a8a3..06f79d0 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,4 +1,4 @@
-From buildd at field.debian.org Wed Jun 08 11:03:59 2011
+From buildd at field.debian.org Sun Sep 11 01:18:47 2011
Return-path: <buildd at field.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,38 +6,38 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1QUGYJ-0007Ig-9x
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:03:59 +0000
+ id 1R2Yh5-0006AQ-Ab
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:18:47 +0000
Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1QUGYI-0000Hn-Fw; Wed, 08 Jun 2011 11:03:58 +0000
+ id 1R2Yh4-0004Q5-33; Sun, 11 Sep 2011 01:18:46 +0000
Received: from buildd by field.debian.org with local (Exim 4.72)
(envelope-from <buildd at field.debian.org>)
- id 1QUGYH-0008Ek-NK; Wed, 08 Jun 2011 11:03:57 +0000
-Message-Id: <E1QUGYH-0008Ek-NK at field.debian.org>
+ id 1R2Yh3-000GBI-56; Sun, 11 Sep 2011 01:18:45 +0000
+Message-Id: <E1R2Yh3-000GBI-56 at field.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 8 Jun 2011 11:03:57 +0000
+Date: Sun, 11 Sep 2011 01:18:45 +0000
From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.13.1-1 on kfreebsd-i386
(dist=sid)
-Key-Id: 22C61858
+Key-Id: 6B8016EE
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (kfreebsd-i386) 08 Jun 2011 10:59 ║
+║ bedtools 2.13.1-1 (kfreebsd-i386) 11 Sep 2011 01:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: kfreebsd-i386
Hit http://ftp.gr.debian.org sid InRelease
Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
@@ -51,7 +51,7 @@ Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 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
+Get:1 http://incoming.debian.org Release.gpg [836 B]
Ign http://ftp.gr.debian.org sid/contrib Translation-en
Ign http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
@@ -63,12 +63,13 @@ 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://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [32.0 kB]
+Get:4 http://incoming.debian.org Packages [290 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
+Fetched 325 kB in 5s (61.4 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,11 +90,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 2s (284 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 2s (330 kB/s)
Download complete and in download only mode
Check arch
@@ -107,18 +108,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.17-1)
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 15 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 15 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -127,38 +128,38 @@ Checking correctness of dependencies...
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, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.1-4)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+freebsd-utils: already installed (8.2+ds2-5)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -168,8 +169,8 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
procmail graphviz
@@ -178,29 +179,27 @@ 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 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 11 not upgraded.
-Need to get 0 B/9216 kB of archives.
-After this operation, 25.7 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 15 not upgraded.
+Need to get 0 B/9053 kB of archives.
+After this operation, 25.8 MB of additional disk space will be used.
+Selecting previously deselected package libpipeline1.
+(Reading database ... 12163 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
Selecting previously deselected package groff-base.
-(Reading database ... 12194 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_5.08-1_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -210,40 +209,39 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
Setting up groff-base (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -251,11 +249,11 @@ 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 15 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.52.20110606-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-11 gcc-4.6_4.6.0-11 kfreebsd-kernel-headers_0.54 libc0.1-dev_2.13-5 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-11 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.6.0-5 g++-4.6_4.6.0-11 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-11 gcc-4.6-base_4.6.0-11 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.54 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-5 libc-dev-bin_2.13-5 libc0.1_2.13-5 libc0.1-dev_2.13-5 libcam0_8.2-1 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-11 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.2-1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-11 libgpg-error0_1.10-0.3 libkiconv4_8.2-1 libkvm0_8.2-1 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-2 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-11 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-2 libsbuf0_8.2-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-11 libstdc++6-4.6-dev_4.6.0-11 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 ufsutils_8.2-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-19 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.17-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-19 libc-dev-bin_2.13-19 libc0.1_2.13-19 libc0.1-dev_2.13-19 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-19 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -266,12 +264,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -287,24 +285,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -315,22 +313,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1/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_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -344,9 +343,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -364,21 +360,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -391,7 +427,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -417,17 +453,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -438,11 +463,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -470,6 +490,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -482,9 +515,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -519,6 +552,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -533,7 +573,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -542,6 +582,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -576,59 +617,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.12.0-1_kfreebsd-i386.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1103
+Build finished at 20110911-0117
-bedtools_2.12.0-1_kfreebsd-i386.changes:
+bedtools_2.13.1-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- e5fd8770a2d1ba023aa395c44a4904b8245c9a56 1616430 bedtools_2.12.0-1_kfreebsd-i386.deb
+ 7f82b478da9ac213d02bb6d2a2f4ac597eda2f45 658382 bedtools_2.13.1-1_kfreebsd-i386.deb
Checksums-Sha256:
- 0af9565473d99b74de832662667d0c34abe97ec338ca8a9e5021c5728fe09c20 1616430 bedtools_2.12.0-1_kfreebsd-i386.deb
+ 41ce144abfca6cb751d55a393a8d9f6b840cee9d31bd0ed048c2e6528c2e8185 658382 bedtools_2.13.1-1_kfreebsd-i386.deb
Files:
- b8e239a745721a790a6399ec653be0bf 1616430 science optional bedtools_2.12.0-1_kfreebsd-i386.deb
+ 5ba65e4ba601613400dc91240d96771f 658382 science optional bedtools_2.13.1-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_kfreebsd-i386.deb
+bedtools_2.13.1-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 1616430 bytes: control archive= 1662 bytes.
- 772 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 658382 bytes: control archive= 1730 bytes.
+ 845 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3622
- Depends: libc0.1 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4790
+ Depends: libc0.1 (>= 2.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -638,49 +684,52 @@ bedtools_2.12.0-1_kfreebsd-i386.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 11:00 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-08 11:03 ./usr/bin/
--rwxr-xr-x root/root 166108 2011-06-08 11:03 ./usr/bin/annotateBed
--rwxr-xr-x root/root 118516 2011-06-08 11:03 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96344 2011-06-08 11:03 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 130964 2011-06-08 11:03 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121112 2011-06-08 11:03 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120928 2011-06-08 11:03 ./usr/bin/closestBed
--rwxr-xr-x root/root 105292 2011-06-08 11:03 ./usr/bin/complementBed
--rwxr-xr-x root/root 171284 2011-06-08 11:03 ./usr/bin/coverageBed
--rwxr-xr-x root/root 141500 2011-06-08 11:03 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 141500 2011-06-08 11:03 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 196960 2011-06-08 11:03 ./usr/bin/fjoin
--rwxr-xr-x root/root 113864 2011-06-08 11:03 ./usr/bin/flankBed
--rwxr-xr-x root/root 184240 2011-06-08 11:03 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 190692 2011-06-08 11:03 ./usr/bin/intersectBed
--rwxr-xr-x root/root 106340 2011-06-08 11:03 ./usr/bin/linksBed
--rwxr-xr-x root/root 108664 2011-06-08 11:03 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 108640 2011-06-08 11:03 ./usr/bin/mergeBed
--rwxr-xr-x root/root 88152 2011-06-08 11:03 ./usr/bin/overlap
--rwxr-xr-x root/root 252408 2011-06-08 11:03 ./usr/bin/pairToBed
--rwxr-xr-x root/root 176544 2011-06-08 11:03 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129244 2011-06-08 11:03 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105004 2011-06-08 11:03 ./usr/bin/slopBed
--rwxr-xr-x root/root 143628 2011-06-08 11:03 ./usr/bin/sortBed
--rwxr-xr-x root/root 113456 2011-06-08 11:03 ./usr/bin/subtractBed
--rwxr-xr-x root/root 63600 2011-06-08 11:03 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 174288 2011-06-08 11:03 ./usr/bin/windowBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-09-11 01:17 ./usr/bin/
+-rwxr-xr-x root/root 102368 2011-09-11 01:17 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 220316 2011-09-11 01:17 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96344 2011-09-11 01:17 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227616 2011-09-11 01:17 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 120944 2011-09-11 01:17 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 119332 2011-09-11 01:17 ./usr/bin/closestBed
+-rwxr-xr-x root/root 104548 2011-09-11 01:17 ./usr/bin/complementBed
+-rwxr-xr-x root/root 277908 2011-09-11 01:17 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 141568 2011-09-11 01:17 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 112732 2011-09-11 01:17 ./usr/bin/flankBed
+-rwxr-xr-x root/root 293744 2011-09-11 01:17 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 301404 2011-09-11 01:17 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 104864 2011-09-11 01:17 ./usr/bin/linksBed
+-rwxr-xr-x root/root 108680 2011-09-11 01:17 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 106240 2011-09-11 01:17 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297300 2011-09-11 01:17 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 141616 2011-09-11 01:17 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88152 2011-09-11 01:17 ./usr/bin/overlap
+-rwxr-xr-x root/root 366956 2011-09-11 01:17 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178272 2011-09-11 01:17 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129148 2011-09-11 01:17 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 104540 2011-09-11 01:17 ./usr/bin/slopBed
+-rwxr-xr-x root/root 141928 2011-09-11 01:17 ./usr/bin/sortBed
+-rwxr-xr-x root/root 268636 2011-09-11 01:17 ./usr/bin/tagBam
+-rwxr-xr-x root/root 112704 2011-09-11 01:17 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 59508 2011-09-11 01:17 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 281908 2011-09-11 01:17 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -694,21 +743,21 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1307530744-28969/build/buildd-bedtools_2.12.0-1-kfreebsd-i386-GvXhl7
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1315703583-59249/build/buildd-bedtools_2.13.1-1-kfreebsd-i386-atotGL
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 15 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* libglib2.0-0* libmagic1* libpcre3*
+ html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 11 not upgraded.
-After this operation, 25.7 MB disk space will be freed.
-(Reading database ... 13559 files and directories currently installed.)
+0 upgraded, 0 newly installed, 19 to remove and 15 not upgraded.
+After this operation, 25.8 MB disk space will be freed.
+(Reading database ... 13513 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -731,8 +780,6 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -746,18 +793,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 72050
-Build-Time: 155
+Build-Space: 92724
+Build-Time: 180
Distribution: sid
-Install-Time: 77
-Job: bedtools_2.12.0-1
+Install-Time: 80
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 252
-Source-Version: 2.12.0-1
-Space: 72050
+Package-Time: 286
+Source-Version: 2.13.1-1
+Space: 92724
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1103
-Build needed 00:04:12, 72050k disc space
-Signature with key '22C61858' requested:
+Finished at 20110911-0117
+Build needed 00:04:46, 92724k disc space
+Signature with key '6B8016EE' requested:
diff --git a/mips.log b/mips.log
index 04e6fca..4ff8e02 100644
--- a/mips.log
+++ b/mips.log
@@ -1,68 +1,67 @@
-From buildd at lucatelli.debian.org Wed Jun 08 11:36:44 2011
-Return-path: <buildd at lucatelli.debian.org>
+From buildd at ball.debian.org Sun Sep 11 01:29:33 2011
+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 <buildd at lucatelli.debian.org>)
- id 1QUH3z-0003p6-RG
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:36:44 +0000
-Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1R2YrV-0007pq-IZ
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:29:33 +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=lucatelli.debian.org,
- EMAIL=hostmaster at lucatelli.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 <buildd at lucatelli.debian.org>)
- id 1QUH3x-0002ol-SH
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:36:42 +0000
-Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lucatelli.debian.org>) id 1QUH3n-0003re-SA
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:36:31 +0000
-From: buildd on lucatelli <buildd at lucatelli.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on mips (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1R2YrU-0008N4-19
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:29:32 +0000
+Received: from buildd by ball.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at ball.debian.org>)
+ id 1R2YrS-0004oo-Mm; Sun, 11 Sep 2011 01:29:30 +0000
+Date: Sun, 11 Sep 2011 01:29:30 +0000
+Message-Id: <E1R2YrS-0004oo-Mm 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_2.13.1-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QUH3n-0003re-SA at lucatelli.debian.org>
-Date: Wed, 08 Jun 2011 11:36:31 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (mips) 08 Jun 2011 11:04 ║
+║ bedtools 2.13.1-1 (mips) 11 Sep 2011 01:07 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5287 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5755 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 [5287 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [49.7 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [92.0 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7164 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [54.3 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [92.0 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7164 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [54.3 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5755 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [57.4 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [102 kB]
+Get:8 http://ftp.de.debian.org unstable/main mips Packages [7480 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib mips Packages [56.1 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7480 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [56.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [48.8 kB]
-Get:18 http://incoming.debian.org Packages [468 kB]
+Get:17 http://incoming.debian.org Sources [32.0 kB]
+Get:18 http://incoming.debian.org Packages [290 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.1 MB in 1min 15s (345 kB/s)
+Fetched 27.5 MB in 1min 16s (360 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +82,11 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 1s (517 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 1s (549 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,38 +120,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-4)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-20)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -174,51 +173,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 13 not upgraded.
-Need to get 9596 kB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-2 [35.5 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-1 [1005 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-3 [859 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
+Need to get 9543 kB of archives.
+After this operation, 30.3 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.08-1 [250 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main file mips 5.08-1 [51.8 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-4 [142 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-4 [858 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-4 [2025 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9596 kB in 1s (5627 kB/s)
+Fetched 9543 kB in 2s (4019 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10620 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10619 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mips.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_mips.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mips.deb) ...
+Unpacking file (from .../archives/file_5.08-1_mips.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mips.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -228,43 +227,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mips.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -272,11 +271,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.51.20110523-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-10 gcc-4.6_4.6.0-10 libc6-dev_2.13-4 libstdc++6_4.6.0-10 libstdc++6-4.6-dev_4.6.0-10 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110523-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-10 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-10 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-10 gcc-4.6-base_4.6.0-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-10 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-10 libstdc++6-4.6-dev_4.6.0-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mips (mips64)
+Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-20 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -286,14 +285,13 @@ Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,39 +301,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -344,36 +333,25 @@ No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
debian/rules build
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1/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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -387,9 +365,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -407,21 +382,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -434,7 +449,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -460,17 +475,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -481,11 +485,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -513,6 +512,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -525,9 +537,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -562,6 +574,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -576,19 +595,16 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mips-LNLqjG/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mips-JdsEXM/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -623,59 +639,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../bedtools_2.12.0-1_mips.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_mips.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1136
+Build finished at 20110911-0129
-bedtools_2.12.0-1_mips.changes:
+bedtools_2.13.1-1_mips.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli 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
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 35a3355d4ad7585c016b303122e2848975548c1b 1540856 bedtools_2.12.0-1_mips.deb
+ 876281e77d10c1a0d091e715cf03abe79fd114a0 581984 bedtools_2.13.1-1_mips.deb
Checksums-Sha256:
- e72e3a8c4f0dc0aba6acaac39dff50824358b440562a1d519f0b3d9931381a15 1540856 bedtools_2.12.0-1_mips.deb
+ e1249e7783a9cd23a20ce96423c01af0676bbcb6a1808d568a672f4b7c3da822 581984 bedtools_2.13.1-1_mips.deb
Files:
- fb0db7c2aa9057fe902a3fd33da33b40 1540856 science optional bedtools_2.12.0-1_mips.deb
+ 28fb1b6c4b53a7b1525fab1602cd17f8 581984 science optional bedtools_2.13.1-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_mips.deb
+bedtools_2.13.1-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 1540856 bytes: control archive= 1653 bytes.
- 760 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 581984 bytes: control archive= 1728 bytes.
+ 834 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3976
+ Installed-Size: 5112
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -685,49 +706,52 @@ bedtools_2.12.0-1_mips.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 11:34 ./
-drwxr-xr-x root/root 0 2011-06-08 11:35 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:35 ./usr/bin/
--rwxr-xr-x root/root 66488 2011-06-08 11:35 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 188204 2011-06-08 11:35 ./usr/bin/coverageBed
--rwxr-xr-x root/root 149804 2011-06-08 11:35 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 206620 2011-06-08 11:35 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113176 2011-06-08 11:35 ./usr/bin/complementBed
--rwxr-xr-x root/root 135656 2011-06-08 11:35 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 94344 2011-06-08 11:35 ./usr/bin/overlap
--rwxr-xr-x root/root 115832 2011-06-08 11:35 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 102648 2011-06-08 11:35 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 182092 2011-06-08 11:35 ./usr/bin/annotateBed
--rwxr-xr-x root/root 129820 2011-06-08 11:35 ./usr/bin/bamToBed
--rwxr-xr-x root/root 114168 2011-06-08 11:35 ./usr/bin/linksBed
--rwxr-xr-x root/root 140556 2011-06-08 11:35 ./usr/bin/bedToBam
--rwxr-xr-x root/root 149788 2011-06-08 11:35 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 185400 2011-06-08 11:35 ./usr/bin/pairToPair
--rwxr-xr-x root/root 126936 2011-06-08 11:35 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 271900 2011-06-08 11:35 ./usr/bin/pairToBed
--rwxr-xr-x root/root 150232 2011-06-08 11:35 ./usr/bin/sortBed
--rwxr-xr-x root/root 188812 2011-06-08 11:35 ./usr/bin/windowBed
--rwxr-xr-x root/root 119544 2011-06-08 11:35 ./usr/bin/flankBed
--rwxr-xr-x root/root 116696 2011-06-08 11:35 ./usr/bin/mergeBed
--rwxr-xr-x root/root 112088 2011-06-08 11:35 ./usr/bin/slopBed
--rwxr-xr-x root/root 119528 2011-06-08 11:35 ./usr/bin/subtractBed
--rwxr-xr-x root/root 126712 2011-06-08 11:35 ./usr/bin/closestBed
--rwxr-xr-x root/root 213580 2011-06-08 11:35 ./usr/bin/fjoin
--rwxr-xr-x root/root 201452 2011-06-08 11:35 ./usr/bin/genomeCoverageBed
-drwxr-xr-x root/root 0 2011-06-08 11:35 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:35 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 11:07 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-06-08 11:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:35 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2011-09-11 01:28 ./usr/bin/
+-rwxr-xr-x root/root 111592 2011-09-11 01:28 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 103448 2011-09-11 01:28 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 114088 2011-09-11 01:28 ./usr/bin/linksBed
+-rwxr-xr-x root/root 127304 2011-09-11 01:28 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 294892 2011-09-11 01:28 ./usr/bin/tagBam
+-rwxr-xr-x root/root 135656 2011-09-11 01:28 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 303692 2011-09-11 01:28 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 118456 2011-09-11 01:28 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 116104 2011-09-11 01:28 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 152732 2011-09-11 01:28 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 151640 2011-09-11 01:28 ./usr/bin/sortBed
+-rwxr-xr-x root/root 63016 2011-09-11 01:28 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 326428 2011-09-11 01:28 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 320172 2011-09-11 01:28 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 244348 2011-09-11 01:28 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 187160 2011-09-11 01:28 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 152780 2011-09-11 01:28 ./usr/bin/nucBed
+-rwxr-xr-x root/root 126648 2011-09-11 01:28 ./usr/bin/closestBed
+-rwxr-xr-x root/root 311420 2011-09-11 01:28 ./usr/bin/windowBed
+-rwxr-xr-x root/root 93608 2011-09-11 01:28 ./usr/bin/overlap
+-rwxr-xr-x root/root 119864 2011-09-11 01:28 ./usr/bin/flankBed
+-rwxr-xr-x root/root 241532 2011-09-11 01:28 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 119656 2011-09-11 01:28 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 328172 2011-09-11 01:28 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 112344 2011-09-11 01:28 ./usr/bin/slopBed
+-rwxr-xr-x root/root 390844 2011-09-11 01:28 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 113096 2011-09-11 01:28 ./usr/bin/complementBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -741,7 +765,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-5e58fc61-1737-4c4b-b48c-af309415d0c5/build/buildd-bedtools_2.12.0-1-mips-LNLqjG
+Purging /var/lib/schroot/mount/sid-mips-sbuild-14fc924b-d274-429b-972e-cbe99af6238b/build/buildd-bedtools_2.13.1-1-mips-JdsEXM
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -749,76 +773,81 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 75544
-Build-Time: 1707
+Build-Space: 99468
+Build-Time: 1068
Distribution: sid
-Install-Time: 73
-Job: bedtools_2.12.0-1
+Install-Time: 93
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 1903
-Source-Version: 2.12.0-1
-Space: 75544
+Package-Time: 1289
+Source-Version: 2.13.1-1
+Space: 99468
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1136
-Build needed 00:31:43, 75544k disc space
-Signature with key 'F4C69470' requested:
+Finished at 20110911-0129
+Build needed 00:21:29, 99468k disc space
+Signature with key '2D578AB1' requested:
-From buildd at monteverdi.ayous.org Wed Jun 08 12:29:17 2011
+From buildd at monteverdi.ayous.org Sun Sep 11 01:31:13 2011
Return-path: <buildd at monteverdi.ayous.org>
-Received: from monteverdi.ayous.org ([2001:a60:f006:deb:20a:1ff:fe00:987])
- by grieg.debian.org with esmtp (Exim 4.72)
- (envelope-from <buildd at monteverdi.ayous.org>) id 1QUHsp-0002Nh-G3
- for logs at buildd.debian.org; Wed, 08 Jun 2011 12:29:17 +0000
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+ (Exim 4.72) (envelope-from <buildd at monteverdi.ayous.org>)
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- id 1QUHsj-000322-1o; Wed, 08 Jun 2011 12:29:09 +0000
+ id 1R2Yts-0005cc-9E; Sun, 11 Sep 2011 01:32:00 +0000
+Date: Sun, 11 Sep 2011 01:32:00 +0000
+Message-Id: <E1R2Yts-0005cc-9E at monteverdi.ayous.org>
From: buildd on monteverdi <buildd at monteverdi.ayous.org>
To: aba+buildd_monteverdi at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.13.1-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QUHsj-000322-1o at monteverdi.ayous.org>
-Date: Wed, 08 Jun 2011 12:29:09 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on monteverdi.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on monteverdi.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (mipsel) 08 Jun 2011 12:09 ║
+║ bedtools 2.13.1-1 (mipsel) 11 Sep 2011 01:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-e4f34d9d-65ac-453f-945e-44586074a8da/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT
-Start Time: 20110608-1209
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Ign http://mirror.ayous.org unstable InRelease
+Ign http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:2 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:3 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:1 http://mirror.ayous.org unstable Release.gpg [836 B]
+Get:2 http://mirror.ayous.org unstable Release [145 kB]
Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:4 http://mirror.ayous.org unstable/main TranslationIndex [2264 B]
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable/main Sources [6666 kB]
-Get:7 http://mirror.ayous.org unstable/main Sources [6666 kB]
-Get:8 http://incoming.debian.org unstable/contrib Sources [58.8 kB]
-Get:9 http://incoming.debian.org unstable/non-free Sources [110 kB]
-Get:10 http://incoming.debian.org unstable/main mipsel Packages [9431 kB]
-Get:11 http://mirror.ayous.org unstable/contrib Sources [58.8 kB]
-Get:12 http://mirror.ayous.org unstable/non-free Sources [110 kB]
-Get:13 http://mirror.ayous.org unstable/main mipsel Packages [9431 kB]
-Get:14 http://incoming.debian.org unstable/contrib mipsel Packages [66.0 kB]
-Get:15 http://incoming.debian.org Release [1604 B]
-Get:16 http://incoming.debian.org Sources [59.9 kB]
-Get:17 http://incoming.debian.org Packages [680 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:18 http://mirror.ayous.org unstable/contrib mipsel Packages [66.0 kB]
+Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:4 http://mirror.ayous.org unstable/main Sources [7228 kB]
+Get:5 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://incoming.debian.org unstable Release [145 kB]
+Get:8 http://mirror.ayous.org unstable/contrib Sources [68.3 kB]
+Get:9 http://mirror.ayous.org unstable/non-free Sources [123 kB]
+Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9811 kB]
+Get:11 http://incoming.debian.org Release [1604 B]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:12 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org unstable/main Sources [7228 kB]
+Get:14 http://incoming.debian.org unstable/contrib Sources [68.3 kB]
+Get:15 http://incoming.debian.org unstable/non-free Sources [123 kB]
+Get:16 http://incoming.debian.org unstable/main mipsel Packages [9811 kB]
+Get:17 http://mirror.ayous.org unstable/contrib mipsel Packages [68.6 kB]
Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:18 http://incoming.debian.org unstable/contrib mipsel Packages [68.6 kB]
+Get:19 http://incoming.debian.org Sources [37.2 kB]
+Get:20 http://incoming.debian.org Packages [464 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 33.7 MB in 45s (738 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 35.4 MB in 45s (781 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -839,30 +868,79 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 3s (243 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 2s (242 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18-1)
+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 1 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+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, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.5-1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.4-4)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -881,51 +959,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 49 not upgraded.
-Need to get 9564 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 1 not upgraded.
+Need to get 9492 kB of archives.
After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-2 [35.6 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.08-1 [248 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.08-1 [51.7 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-4 [133 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-4 [858 kB]
Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-4 [2008 kB]
Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9564 kB in 1s (4916 kB/s)
+Fetched 9492 kB in 1s (5626 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10771 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 11410 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_mipsel.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
+Unpacking file (from .../file_5.08-1_mipsel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -935,51 +1013,55 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.33-rc7 mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-2 dpkg-dev_1.16.0.2 linux-libc-dev_2.6.38-4 gcc-4.6_4.6.0-6 g++-4.6_4.6.0-6 binutils_2.21.51.20110421-3 libstdc++6-4.6-dev_4.6.0-6 libstdc++6_4.6.0-6
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.4_4.4.6-2 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4_4.4.6-2 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-7 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.39-2-loongson-2e mipsel (mips64)
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -989,14 +1071,13 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1012,24 +1093,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1040,22 +1121,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1/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_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1069,9 +1151,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -1089,21 +1168,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -1116,7 +1235,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -1142,17 +1261,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -1163,11 +1271,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -1195,6 +1298,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -1207,9 +1323,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -1244,6 +1360,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -1258,15 +1381,16 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -1301,59 +1425,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bedtools_2.12.0-1_mipsel.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1229
+Build finished at 20110911-0131
-bedtools_2.12.0-1_mipsel.changes:
+bedtools_2.13.1-1_mipsel.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 6491b7bbbcf537ca7f005000af431015f189a729 1533984 bedtools_2.12.0-1_mipsel.deb
+ 5ca48989df8e773bc3389ee3a7a79f1af9ebfb53 614842 bedtools_2.13.1-1_mipsel.deb
Checksums-Sha256:
- 7de4efc2d8987deef32069517e5dd900b873564924861bf6365422cf3e2d690d 1533984 bedtools_2.12.0-1_mipsel.deb
+ ce8ef1c1895a62117bc65d9cfe50d772f279df59f080f658aec5fb3f60ef1118 614842 bedtools_2.13.1-1_mipsel.deb
Files:
- f3719e3f112a096cd6a4024aaf0a5159 1533984 science optional bedtools_2.12.0-1_mipsel.deb
+ fb40c1caa9bea0eed63b57b0d7d3bbd9 614842 science optional bedtools_2.13.1-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_mipsel.deb
+bedtools_2.13.1-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 1533984 bytes: control archive= 1654 bytes.
- 762 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 614842 bytes: control archive= 1722 bytes.
+ 836 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3952
+ Installed-Size: 5004
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -1363,49 +1492,52 @@ bedtools_2.12.0-1_mipsel.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 12:12 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/bin/
--rwxr-xr-x root/root 135400 2011-06-08 12:28 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 149164 2011-06-08 12:28 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 181612 2011-06-08 12:28 ./usr/bin/annotateBed
--rwxr-xr-x root/root 186188 2011-06-08 12:28 ./usr/bin/coverageBed
--rwxr-xr-x root/root 126936 2011-06-08 12:28 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126712 2011-06-08 12:28 ./usr/bin/closestBed
--rwxr-xr-x root/root 115160 2011-06-08 12:28 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 128508 2011-06-08 12:28 ./usr/bin/bamToBed
--rwxr-xr-x root/root 118952 2011-06-08 12:28 ./usr/bin/flankBed
--rwxr-xr-x root/root 205836 2011-06-08 12:28 ./usr/bin/intersectBed
--rwxr-xr-x root/root 211580 2011-06-08 12:28 ./usr/bin/fjoin
--rwxr-xr-x root/root 269036 2011-06-08 12:28 ./usr/bin/pairToBed
--rwxr-xr-x root/root 188284 2011-06-08 12:28 ./usr/bin/windowBed
--rwxr-xr-x root/root 201452 2011-06-08 12:28 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 116200 2011-06-08 12:28 ./usr/bin/mergeBed
--rwxr-xr-x root/root 66488 2011-06-08 12:28 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 112648 2011-06-08 12:28 ./usr/bin/complementBed
--rwxr-xr-x root/root 149180 2011-06-08 12:28 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 94200 2011-06-08 12:28 ./usr/bin/overlap
--rwxr-xr-x root/root 112296 2011-06-08 12:28 ./usr/bin/linksBed
--rwxr-xr-x root/root 111656 2011-06-08 12:28 ./usr/bin/slopBed
--rwxr-xr-x root/root 149224 2011-06-08 12:28 ./usr/bin/sortBed
--rwxr-xr-x root/root 182680 2011-06-08 12:28 ./usr/bin/pairToPair
--rwxr-xr-x root/root 102168 2011-06-08 12:28 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 140556 2011-06-08 12:28 ./usr/bin/bedToBam
--rwxr-xr-x root/root 119080 2011-06-08 12:28 ./usr/bin/subtractBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/bin/
+-rwxr-xr-x root/root 187160 2011-09-11 01:31 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 152780 2011-09-11 01:31 ./usr/bin/nucBed
+-rwxr-xr-x root/root 116104 2011-09-11 01:31 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 294892 2011-09-11 01:31 ./usr/bin/tagBam
+-rwxr-xr-x root/root 126648 2011-09-11 01:31 ./usr/bin/closestBed
+-rwxr-xr-x root/root 151640 2011-09-11 01:31 ./usr/bin/sortBed
+-rwxr-xr-x root/root 135656 2011-09-11 01:31 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 390844 2011-09-11 01:31 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 320172 2011-09-11 01:31 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 119656 2011-09-11 01:31 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 113096 2011-09-11 01:31 ./usr/bin/complementBed
+-rwxr-xr-x root/root 328172 2011-09-11 01:31 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 241484 2011-09-11 01:31 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 118456 2011-09-11 01:31 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 127304 2011-09-11 01:31 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 111592 2011-09-11 01:31 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 114088 2011-09-11 01:31 ./usr/bin/linksBed
+-rwxr-xr-x root/root 103448 2011-09-11 01:31 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 311420 2011-09-11 01:31 ./usr/bin/windowBed
+-rwxr-xr-x root/root 112344 2011-09-11 01:31 ./usr/bin/slopBed
+-rwxr-xr-x root/root 244332 2011-09-11 01:31 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 93608 2011-09-11 01:31 ./usr/bin/overlap
+-rwxr-xr-x root/root 63016 2011-09-11 01:31 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 119864 2011-09-11 01:31 ./usr/bin/flankBed
+-rwxr-xr-x root/root 303644 2011-09-11 01:31 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 326428 2011-09-11 01:31 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 152732 2011-09-11 01:31 ./usr/bin/fastaFromBed
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1414,9 +1546,31 @@ drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-e4f34d9d-65ac-453f-945e-44586074a8da/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-cae9f985-c70d-417e-afb1-0cf3707bacf1/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 98944
+Build-Time: 1207
+Distribution: sid
+Install-Time: 80
+Job: bedtools_2.13.1-1
+Package: bedtools
+Package-Time: 1383
+Source-Version: 2.13.1-1
+Space: 98944
+Status: successful
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1229
-Build needed 00:19:33, 75304k disc space
+Finished at 20110911-0131
+Build needed 00:23:03, 98944k disc space
diff --git a/mipsel.log b/mipsel.log
index 941fb5a..9a57233 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,57 +1,62 @@
-From buildd at monteverdi.ayous.org Wed Jun 08 12:29:17 2011
+From buildd at monteverdi.ayous.org Sun Sep 11 01:31:13 2011
Return-path: <buildd at monteverdi.ayous.org>
-Received: from monteverdi.ayous.org ([2001:a60:f006:deb:20a:1ff:fe00:987])
- by grieg.debian.org with esmtp (Exim 4.72)
- (envelope-from <buildd at monteverdi.ayous.org>) id 1QUHsp-0002Nh-G3
- for logs at buildd.debian.org; Wed, 08 Jun 2011 12:29:17 +0000
-Received: from buildd by monteverdi.ayous.org with local (Exim 4.69)
+Received: from monteverdi.ayous.org ([2001:a60:f006:deb:20a:1ff:fe00:987]
+ helo=alius.ayous.org)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at monteverdi.ayous.org>)
+ id 1R2Yt6-0008Mp-1t
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:31:13 +0000
+Received: from buildd by monteverdi.ayous.org with local (Exim 4.72)
(envelope-from <buildd at monteverdi.ayous.org>)
- id 1QUHsj-000322-1o; Wed, 08 Jun 2011 12:29:09 +0000
+ id 1R2Yts-0005cc-9E; Sun, 11 Sep 2011 01:32:00 +0000
+Date: Sun, 11 Sep 2011 01:32:00 +0000
+Message-Id: <E1R2Yts-0005cc-9E at monteverdi.ayous.org>
From: buildd on monteverdi <buildd at monteverdi.ayous.org>
To: aba+buildd_monteverdi at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.13.1-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QUHsj-000322-1o at monteverdi.ayous.org>
-Date: Wed, 08 Jun 2011 12:29:09 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on monteverdi.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on monteverdi.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (mipsel) 08 Jun 2011 12:09 ║
+║ bedtools 2.13.1-1 (mipsel) 11 Sep 2011 01:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-e4f34d9d-65ac-453f-945e-44586074a8da/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT
-Start Time: 20110608-1209
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Ign http://mirror.ayous.org unstable InRelease
+Ign http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:2 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:3 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:1 http://mirror.ayous.org unstable Release.gpg [836 B]
+Get:2 http://mirror.ayous.org unstable Release [145 kB]
Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:4 http://mirror.ayous.org unstable/main TranslationIndex [2264 B]
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable/main Sources [6666 kB]
-Get:7 http://mirror.ayous.org unstable/main Sources [6666 kB]
-Get:8 http://incoming.debian.org unstable/contrib Sources [58.8 kB]
-Get:9 http://incoming.debian.org unstable/non-free Sources [110 kB]
-Get:10 http://incoming.debian.org unstable/main mipsel Packages [9431 kB]
-Get:11 http://mirror.ayous.org unstable/contrib Sources [58.8 kB]
-Get:12 http://mirror.ayous.org unstable/non-free Sources [110 kB]
-Get:13 http://mirror.ayous.org unstable/main mipsel Packages [9431 kB]
-Get:14 http://incoming.debian.org unstable/contrib mipsel Packages [66.0 kB]
-Get:15 http://incoming.debian.org Release [1604 B]
-Get:16 http://incoming.debian.org Sources [59.9 kB]
-Get:17 http://incoming.debian.org Packages [680 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:18 http://mirror.ayous.org unstable/contrib mipsel Packages [66.0 kB]
+Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:4 http://mirror.ayous.org unstable/main Sources [7228 kB]
+Get:5 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://incoming.debian.org unstable Release [145 kB]
+Get:8 http://mirror.ayous.org unstable/contrib Sources [68.3 kB]
+Get:9 http://mirror.ayous.org unstable/non-free Sources [123 kB]
+Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9811 kB]
+Get:11 http://incoming.debian.org Release [1604 B]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:12 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org unstable/main Sources [7228 kB]
+Get:14 http://incoming.debian.org unstable/contrib Sources [68.3 kB]
+Get:15 http://incoming.debian.org unstable/non-free Sources [123 kB]
+Get:16 http://incoming.debian.org unstable/main mipsel Packages [9811 kB]
+Get:17 http://mirror.ayous.org unstable/contrib mipsel Packages [68.6 kB]
Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:18 http://incoming.debian.org unstable/contrib mipsel Packages [68.6 kB]
+Get:19 http://incoming.debian.org Sources [37.2 kB]
+Get:20 http://incoming.debian.org Packages [464 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 33.7 MB in 45s (738 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 35.4 MB in 45s (781 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -72,30 +77,79 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 3s (243 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 2s (242 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18-1)
+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 1 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.5-1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.4-4)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -114,51 +168,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 49 not upgraded.
-Need to get 9564 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 1 not upgraded.
+Need to get 9492 kB of archives.
After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-2 [35.6 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.08-1 [248 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.08-1 [51.7 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-4 [133 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-4 [858 kB]
Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-4 [2008 kB]
Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9564 kB in 1s (4916 kB/s)
+Fetched 9492 kB in 1s (5626 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10771 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 11410 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_mipsel.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
+Unpacking file (from .../file_5.08-1_mipsel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -168,51 +222,55 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.33-rc7 mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-2 dpkg-dev_1.16.0.2 linux-libc-dev_2.6.38-4 gcc-4.6_4.6.0-6 g++-4.6_4.6.0-6 binutils_2.21.51.20110421-3 libstdc++6-4.6-dev_4.6.0-6 libstdc++6_4.6.0-6
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.4_4.4.6-2 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4_4.4.6-2 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-7 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.39-2-loongson-2e mipsel (mips64)
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -222,14 +280,13 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -245,24 +302,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -273,22 +330,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1/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_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -302,9 +360,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -322,21 +377,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -349,7 +444,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -375,17 +470,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -396,11 +480,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -428,6 +507,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -440,9 +532,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -477,6 +569,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -491,15 +590,16 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -534,59 +634,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bedtools_2.12.0-1_mipsel.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1229
+Build finished at 20110911-0131
-bedtools_2.12.0-1_mipsel.changes:
+bedtools_2.13.1-1_mipsel.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 6491b7bbbcf537ca7f005000af431015f189a729 1533984 bedtools_2.12.0-1_mipsel.deb
+ 5ca48989df8e773bc3389ee3a7a79f1af9ebfb53 614842 bedtools_2.13.1-1_mipsel.deb
Checksums-Sha256:
- 7de4efc2d8987deef32069517e5dd900b873564924861bf6365422cf3e2d690d 1533984 bedtools_2.12.0-1_mipsel.deb
+ ce8ef1c1895a62117bc65d9cfe50d772f279df59f080f658aec5fb3f60ef1118 614842 bedtools_2.13.1-1_mipsel.deb
Files:
- f3719e3f112a096cd6a4024aaf0a5159 1533984 science optional bedtools_2.12.0-1_mipsel.deb
+ fb40c1caa9bea0eed63b57b0d7d3bbd9 614842 science optional bedtools_2.13.1-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_mipsel.deb
+bedtools_2.13.1-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 1533984 bytes: control archive= 1654 bytes.
- 762 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 614842 bytes: control archive= 1722 bytes.
+ 836 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3952
+ Installed-Size: 5004
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -596,49 +701,52 @@ bedtools_2.12.0-1_mipsel.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 12:12 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/bin/
--rwxr-xr-x root/root 135400 2011-06-08 12:28 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 149164 2011-06-08 12:28 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 181612 2011-06-08 12:28 ./usr/bin/annotateBed
--rwxr-xr-x root/root 186188 2011-06-08 12:28 ./usr/bin/coverageBed
--rwxr-xr-x root/root 126936 2011-06-08 12:28 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126712 2011-06-08 12:28 ./usr/bin/closestBed
--rwxr-xr-x root/root 115160 2011-06-08 12:28 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 128508 2011-06-08 12:28 ./usr/bin/bamToBed
--rwxr-xr-x root/root 118952 2011-06-08 12:28 ./usr/bin/flankBed
--rwxr-xr-x root/root 205836 2011-06-08 12:28 ./usr/bin/intersectBed
--rwxr-xr-x root/root 211580 2011-06-08 12:28 ./usr/bin/fjoin
--rwxr-xr-x root/root 269036 2011-06-08 12:28 ./usr/bin/pairToBed
--rwxr-xr-x root/root 188284 2011-06-08 12:28 ./usr/bin/windowBed
--rwxr-xr-x root/root 201452 2011-06-08 12:28 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 116200 2011-06-08 12:28 ./usr/bin/mergeBed
--rwxr-xr-x root/root 66488 2011-06-08 12:28 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 112648 2011-06-08 12:28 ./usr/bin/complementBed
--rwxr-xr-x root/root 149180 2011-06-08 12:28 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 94200 2011-06-08 12:28 ./usr/bin/overlap
--rwxr-xr-x root/root 112296 2011-06-08 12:28 ./usr/bin/linksBed
--rwxr-xr-x root/root 111656 2011-06-08 12:28 ./usr/bin/slopBed
--rwxr-xr-x root/root 149224 2011-06-08 12:28 ./usr/bin/sortBed
--rwxr-xr-x root/root 182680 2011-06-08 12:28 ./usr/bin/pairToPair
--rwxr-xr-x root/root 102168 2011-06-08 12:28 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 140556 2011-06-08 12:28 ./usr/bin/bedToBam
--rwxr-xr-x root/root 119080 2011-06-08 12:28 ./usr/bin/subtractBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/bin/
+-rwxr-xr-x root/root 187160 2011-09-11 01:31 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 152780 2011-09-11 01:31 ./usr/bin/nucBed
+-rwxr-xr-x root/root 116104 2011-09-11 01:31 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 294892 2011-09-11 01:31 ./usr/bin/tagBam
+-rwxr-xr-x root/root 126648 2011-09-11 01:31 ./usr/bin/closestBed
+-rwxr-xr-x root/root 151640 2011-09-11 01:31 ./usr/bin/sortBed
+-rwxr-xr-x root/root 135656 2011-09-11 01:31 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 390844 2011-09-11 01:31 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 320172 2011-09-11 01:31 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 119656 2011-09-11 01:31 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 113096 2011-09-11 01:31 ./usr/bin/complementBed
+-rwxr-xr-x root/root 328172 2011-09-11 01:31 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 241484 2011-09-11 01:31 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 118456 2011-09-11 01:31 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 127304 2011-09-11 01:31 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 111592 2011-09-11 01:31 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 114088 2011-09-11 01:31 ./usr/bin/linksBed
+-rwxr-xr-x root/root 103448 2011-09-11 01:31 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 311420 2011-09-11 01:31 ./usr/bin/windowBed
+-rwxr-xr-x root/root 112344 2011-09-11 01:31 ./usr/bin/slopBed
+-rwxr-xr-x root/root 244332 2011-09-11 01:31 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 93608 2011-09-11 01:31 ./usr/bin/overlap
+-rwxr-xr-x root/root 63016 2011-09-11 01:31 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 119864 2011-09-11 01:31 ./usr/bin/flankBed
+-rwxr-xr-x root/root 303644 2011-09-11 01:31 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 326428 2011-09-11 01:31 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 152732 2011-09-11 01:31 ./usr/bin/fastaFromBed
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-09-11 01:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:11 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -647,9 +755,31 @@ drwxr-xr-x root/root 0 2011-06-08 12:28 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-e4f34d9d-65ac-453f-945e-44586074a8da/build/buildd-bedtools_2.12.0-1-mipsel-qzsuKT
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-cae9f985-c70d-417e-afb1-0cf3707bacf1/build/buildd-bedtools_2.13.1-1-mipsel-pXOGRI
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 98944
+Build-Time: 1207
+Distribution: sid
+Install-Time: 80
+Job: bedtools_2.13.1-1
+Package: bedtools
+Package-Time: 1383
+Source-Version: 2.13.1-1
+Space: 98944
+Status: successful
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1229
-Build needed 00:19:33, 75304k disc space
+Finished at 20110911-0131
+Build needed 00:23:03, 98944k disc space
diff --git a/powerpc.log b/powerpc.log
index 1446965..e25719f 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at porpora.debian.org Wed Jun 08 11:02:46 2011
-Return-path: <buildd at porpora.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at poulenc.debian.org Sun Sep 11 01:14:19 2011
+Return-path: <buildd at poulenc.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1QUGX7-0007Ch-Pm
- for logs at buildd.debian.org; Wed, 08 Jun 2011 11:02:46 +0000
-Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
- helo=porpora.debian.org)
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1R2Ycl-0005co-4G
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:14:19 +0000
+Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
+ helo=poulenc.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1QUGX6-0001nU-Fb; Wed, 08 Jun 2011 11:02:44 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1QUGX5-00051F-T2; Wed, 08 Jun 2011 11:02:43 +0000
-Message-Id: <E1QUGX5-00051F-T2 at porpora.debian.org>
+ CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1R2Yck-0004Ez-Cv; Sun, 11 Sep 2011 01:14:18 +0000
+Received: from buildd by poulenc.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at poulenc.debian.org>)
+ id 1R2Ycj-00038n-Sc; Sun, 11 Sep 2011 01:14:17 +0000
+Message-Id: <E1R2Ycj-00038n-Sc at poulenc.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 8 Jun 2011 11:02:43 +0000
-From: buildd on porpora <buildd at porpora.debian.org>
+Date: Sun, 11 Sep 2011 01:14:17 +0000
+From: buildd on poulenc <buildd at poulenc.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on powerpc (dist=sid)
-Key-Id: CDFA0A89
+Subject: Log for successful build of bedtools_2.13.1-1 on powerpc (dist=sid)
+Key-Id: 779E1DD6
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (powerpc) 08 Jun 2011 10:57 ║
+║ bedtools 2.13.1-1 (powerpc) 11 Sep 2011 01:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: powerpc
Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.uk.debian.org unstable/main Sources [5287 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5755 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://ftp.uk.debian.org unstable/contrib Sources [49.7 kB]
-Get:6 http://ftp.uk.debian.org unstable/non-free Sources [92.0 kB]
-Get:7 http://ftp.uk.debian.org unstable/main powerpc Packages [7275 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [5287 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.1 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5755 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [57.4 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [102 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7585 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.7 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [92.0 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7275 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [54.1 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7585 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.7 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.4 kB]
-Get:18 http://incoming.debian.org Packages [473 kB]
+Get:17 http://incoming.debian.org Sources [32.0 kB]
+Get:18 http://incoming.debian.org Packages [290 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.3 MB in 22s (1171 kB/s)
+Fetched 27.7 MB in 23s (1172 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,13 +81,14 @@ 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 796 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 1s (518 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 1s (489 kB/s)
Download complete and in download only mode
Check arch
@@ -101,15 +102,17 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 18 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
+Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
@@ -119,44 +122,45 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-4)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt 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 libglib2.0-0 libmagic1 libpcre3 libpipeline1
@@ -172,50 +176,50 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
0 upgraded, 21 newly installed, 0 to remove and 18 not upgraded.
-Need to get 9740 kB of archives.
-After this operation, 29.6 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-2 [37.3 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-1 [1020 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5+b1 [240 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-3 [837 kB]
+Need to get 9697 kB of archives.
+After this operation, 29.8 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.08-1 [253 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.08-1 [51.9 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-4 [134 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-4 [837 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-4 [422 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-4 [2032 kB]
Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9740 kB in 1s (7688 kB/s)
+Fetched 9697 kB in 1s (6955 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10610 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 11071 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_powerpc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_powerpc.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_powerpc.deb) ...
+Unpacking file (from .../file_5.08-1_powerpc.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -225,43 +229,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_powerpc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_powerpc.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -272,8 +276,8 @@ Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.51.20110523-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-10 gcc-4.6_4.6.0-10 libc6-dev_2.13-4 libstdc++6_4.6.0-10 libstdc++6-4.6-dev_4.6.0-10 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110523-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-10 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-i18n_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-10 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-10 gcc-4.6-base_4.6.0-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libc6-ppc64_2.13-4 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-10 liblocale-gettext-perl_1.05-6+b2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-10 libstdc++6-4.6-dev_4.6.0-10 libtext-charwidth-perl_0.04-6+b3 libtext-iconv-perl_1.7-2+b2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-8 gcc_4:4.6.1-2 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-6 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-8 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-8 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011h-4 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -284,35 +288,18 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
────────────────
-User Environment
-────────────────
-
-HOME=/home/buildd
-LOGNAME=buildd
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_COMMAND=env
-SCHROOT_GID=1009
-SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-powerpc-sbuild-0da373a2-6d9c-4701-871e-8d4c0e6b85db
-SCHROOT_UID=2952
-SCHROOT_USER=buildd
-SHELL=/bin/sh
-TERM=screen
-USER=buildd
-USERNAME=buildd
-
dpkg-buildpackage
─────────────────
@@ -322,24 +309,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -350,22 +337,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1/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_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -379,9 +367,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -399,21 +384,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -426,7 +451,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -452,17 +477,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -473,11 +487,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -505,6 +514,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -517,9 +539,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -554,6 +576,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -568,7 +597,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -577,6 +606,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -611,59 +641,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.12.0-1_powerpc.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110608-1102
+Build finished at 20110911-0114
-bedtools_2.12.0-1_powerpc.changes:
+bedtools_2.13.1-1_powerpc.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
+Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 5baf6163d3e10d91d947fe88a3725905f9396754 1665434 bedtools_2.12.0-1_powerpc.deb
+ fe4c8c81fffae22cc159ac847da38777fada6f8c 575800 bedtools_2.13.1-1_powerpc.deb
Checksums-Sha256:
- 9735011b07773aa9ee1f64a7a04f405b79589b2edee228746d439423c75a9b64 1665434 bedtools_2.12.0-1_powerpc.deb
+ d32e44d3adb207709ad93e576eb24a673090c851aee0690e9d23609be6b83cca 575800 bedtools_2.13.1-1_powerpc.deb
Files:
- 75791f166ce89a4afdb21ec20d0bc6b6 1665434 science optional bedtools_2.12.0-1_powerpc.deb
+ 347c074a49f4be13d4703e6e1798600b 575800 science optional bedtools_2.13.1-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_powerpc.deb
+bedtools_2.13.1-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 1665434 bytes: control archive= 1648 bytes.
- 763 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 575800 bytes: control archive= 1719 bytes.
+ 837 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3852
+ Installed-Size: 4916
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -673,49 +708,52 @@ bedtools_2.12.0-1_powerpc.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/bin/
--rwxr-xr-x root/root 200940 2011-06-08 11:02 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113436 2011-06-08 11:02 ./usr/bin/mergeBed
--rwxr-xr-x root/root 145652 2011-06-08 11:02 ./usr/bin/sortBed
--rwxr-xr-x root/root 137580 2011-06-08 11:02 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121380 2011-06-08 11:02 ./usr/bin/closestBed
--rwxr-xr-x root/root 146548 2011-06-08 11:02 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 195780 2011-06-08 11:02 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 178564 2011-06-08 11:02 ./usr/bin/annotateBed
--rwxr-xr-x root/root 207244 2011-06-08 11:02 ./usr/bin/fjoin
--rwxr-xr-x root/root 146548 2011-06-08 11:02 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 109700 2011-06-08 11:02 ./usr/bin/complementBed
--rwxr-xr-x root/root 265916 2011-06-08 11:02 ./usr/bin/pairToBed
--rwxr-xr-x root/root 182652 2011-06-08 11:02 ./usr/bin/coverageBed
--rwxr-xr-x root/root 100644 2011-06-08 11:02 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109996 2011-06-08 11:02 ./usr/bin/linksBed
--rwxr-xr-x root/root 109068 2011-06-08 11:02 ./usr/bin/slopBed
--rwxr-xr-x root/root 115596 2011-06-08 11:02 ./usr/bin/subtractBed
--rwxr-xr-x root/root 183572 2011-06-08 11:02 ./usr/bin/windowBed
--rwxr-xr-x root/root 125812 2011-06-08 11:02 ./usr/bin/bamToBed
--rwxr-xr-x root/root 133404 2011-06-08 11:02 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 64844 2011-06-08 11:02 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 179308 2011-06-08 11:02 ./usr/bin/pairToPair
--rwxr-xr-x root/root 122780 2011-06-08 11:02 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 116988 2011-06-08 11:02 ./usr/bin/flankBed
--rwxr-xr-x root/root 112916 2011-06-08 11:02 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92604 2011-06-08 11:02 ./usr/bin/overlap
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-08 10:58 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-08 11:02 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:10 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-09-11 01:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-11 01:14 ./usr/bin/
+-rwxr-xr-x root/root 231864 2011-09-11 01:14 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 122044 2011-09-11 01:14 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 108780 2011-09-11 01:14 ./usr/bin/linksBed
+-rwxr-xr-x root/root 285264 2011-09-11 01:14 ./usr/bin/tagBam
+-rwxr-xr-x root/root 371312 2011-09-11 01:14 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 147500 2011-09-11 01:14 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63764 2011-09-11 01:14 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 314792 2011-09-11 01:14 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 112868 2011-09-11 01:14 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 100644 2011-09-11 01:14 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 108964 2011-09-11 01:14 ./usr/bin/complementBed
+-rwxr-xr-x root/root 174332 2011-09-11 01:14 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 108788 2011-09-11 01:14 ./usr/bin/slopBed
+-rwxr-xr-x root/root 148068 2011-09-11 01:14 ./usr/bin/nucBed
+-rwxr-xr-x root/root 131604 2011-09-11 01:14 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 121116 2011-09-11 01:14 ./usr/bin/closestBed
+-rwxr-xr-x root/root 293440 2011-09-11 01:14 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 108764 2011-09-11 01:14 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 309848 2011-09-11 01:14 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 236012 2011-09-11 01:14 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 297544 2011-09-11 01:14 ./usr/bin/windowBed
+-rwxr-xr-x root/root 112932 2011-09-11 01:14 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 92404 2011-09-11 01:14 ./usr/bin/overlap
+-rwxr-xr-x root/root 115236 2011-09-11 01:14 ./usr/bin/flankBed
+-rwxr-xr-x root/root 114020 2011-09-11 01:14 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 313936 2011-09-11 01:14 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 144012 2011-09-11 01:14 ./usr/bin/sortBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -729,7 +767,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-0da373a2-6d9c-4701-871e-8d4c0e6b85db/build/buildd-bedtools_2.12.0-1-powerpc-Xp8fmS
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-ffcebc77-bfd7-43e3-966c-893136fdc0c0/build/buildd-bedtools_2.13.1-1-powerpc-EOtipC
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -737,18 +775,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 79440
-Build-Time: 254
+Build-Space: 101956
+Build-Time: 252
Distribution: sid
-Install-Time: 41
-Job: bedtools_2.12.0-1
+Install-Time: 43
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 332
-Source-Version: 2.12.0-1
-Space: 79440
+Package-Time: 336
+Source-Version: 2.13.1-1
+Space: 101956
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110608-1102
-Build needed 00:05:32, 79440k disc space
-Signature with key 'CDFA0A89' requested:
+Finished at 20110911-0114
+Build needed 00:05:36, 101956k disc space
+Signature with key '779E1DD6' requested:
diff --git a/s390.log b/s390.log
index 462ed33..9875306 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Thu Jun 09 22:29:57 2011
+From buildd at zandonai.debian.org Sun Sep 11 01:23:46 2011
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,
@@ -6,64 +6,64 @@ 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 zandonai.debian.org>)
- id 1QUnjh-0006ar-LE
- for logs at buildd.debian.org; Thu, 09 Jun 2011 22:29:57 +0000
+ id 1R2Yls-0006xz-KQ
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 01:23:45 +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=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 zandonai.debian.org>)
- id 1QUnjg-0002B1-Cm; Thu, 09 Jun 2011 22:29:56 +0000
+ id 1R2Ylr-00088S-Cg; Sun, 11 Sep 2011 01:23:43 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1QUnjf-00045C-Uu; Thu, 09 Jun 2011 22:29:55 +0000
-Message-Id: <E1QUnjf-00045C-Uu at zandonai.debian.org>
+ id 1R2Ylq-0008Ny-Up; Sun, 11 Sep 2011 01:23:42 +0000
+Message-Id: <E1R2Ylq-0008Ny-Up 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: Thu, 9 Jun 2011 22:29:55 +0000
+Date: Sun, 11 Sep 2011 01:23:42 +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_2.12.0-1 on s390 (dist=sid)
-Key-Id: 9BD94C88
+Subject: Log for successful build of bedtools_2.13.1-1 on s390 (dist=sid)
+Key-Id: 2D941D26
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (s390) 09 Jun 2011 22:26 ║
+║ bedtools 2.13.1-1 (s390) 11 Sep 2011 01:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5291 kB]
+Get:2 http://ftp.de.debian.org unstable/main Sources [5755 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 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 [5291 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [49.7 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [92.5 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7190 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [53.0 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5755 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [57.4 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [102 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7491 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.8 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [92.5 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7190 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [53.0 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7491 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [33.7 kB]
-Get:18 http://incoming.debian.org Packages [383 kB]
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [290 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.1 MB in 24s (1055 kB/s)
+Fetched 27.5 MB in 24s (1136 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ 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 796 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 0s (2003 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 1s (435 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,38 +122,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-4)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-20)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,51 +175,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 29 not upgraded.
-Need to get 9828 kB of archives.
-After this operation, 29.4 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-2 [38.9 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-1 [1017 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5+b1 [243 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-3 [881 kB]
+0 upgraded, 21 newly installed, 0 to remove and 9 not upgraded.
+Need to get 9829 kB of archives.
+After this operation, 29.7 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.08-1 [255 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.08-1 [52.2 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-4 [143 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-4 [879 kB]
Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.6-1 [1639 kB]
Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4 [431 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-4 [2073 kB]
Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9828 kB in 2s (3535 kB/s)
+Fetched 9829 kB in 2s (3492 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10560 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10552 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_s390.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_s390.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_s390.deb) ...
+Unpacking file (from .../archives/file_5.08-1_s390.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -229,43 +229,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_s390.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_s390.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -273,11 +273,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.51.20110421-6 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-8 gcc-4.6_4.6.0-8 libc6-dev_2.13-4 libstdc++6_4.6.0-8 libstdc++6-4.6-dev_4.6.0-8 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-6 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-8 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-8 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-8 gcc-4.6-base_4.6.0-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-8 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-8 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-8 libstdc++6-4.6-dev_4.6.0-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-20 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -309,24 +309,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -337,22 +337,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1/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_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -366,9 +367,6 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
@@ -386,21 +384,61 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
-BamIndex.cpp: In member function 'virtual bool BamTools::BamDefaultIndex::Load(const string&)':
-BamIndex.cpp:405:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
-BamIndex.cpp: In member function 'virtual bool BamTools::BamToolsIndex::Load(const string&)':
-BamIndex.cpp:818:12: warning: variable 'elementsRead' set but not used [-Wunused-but-set-variable]
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int main(int, char**)':
-annotateMain.cpp:38:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
@@ -413,7 +451,7 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
-bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -439,17 +477,6 @@ bedToBam.cpp:59:10: warning: variable 'haveMapQual' set but not used [-Wunused-b
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
-Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
-Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -460,11 +487,6 @@ Fasta.cpp:32:16: warning: converting to non-pointer type 'int' from NULL [-Wconv
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -492,6 +514,19 @@ mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunu
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
overlap.cpp: In function 'int main(int, char**)':
@@ -504,9 +539,9 @@ pairToBedMain.cpp: In function 'int main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:253:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:254:12: 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:305:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
@@ -541,6 +576,13 @@ subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunu
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
@@ -555,7 +597,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-s390-3rG7yH/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-s390-h0Qq00/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -564,6 +606,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -598,59 +641,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.12.0-1_s390.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110609-2229
+Build finished at 20110911-0123
-bedtools_2.12.0-1_s390.changes:
+bedtools_2.13.1-1_s390.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
Maintainer: s390 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
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 984e4f68d94e37b8556b01d5726cc9e575702193 1607392 bedtools_2.12.0-1_s390.deb
+ b92806928fffe9d4b9514a106bbd6d7a450e33eb 507594 bedtools_2.13.1-1_s390.deb
Checksums-Sha256:
- eec7dcafea2fd18ca7a42e62a532fb86423b0dd11ff6fe6716c95fd4a759914a 1607392 bedtools_2.12.0-1_s390.deb
+ 0785dba1fef198131fd29fe5146670a991d90d5816bb57612dea33e1011e463c 507594 bedtools_2.13.1-1_s390.deb
Files:
- 41026305f770e4169300adbe39b998e7 1607392 science optional bedtools_2.12.0-1_s390.deb
+ be2ce6d3880ce7e913fc9f6cbf9ee531 507594 science optional bedtools_2.13.1-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_s390.deb
+bedtools_2.13.1-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 1607392 bytes: control archive= 1642 bytes.
- 760 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 507594 bytes: control archive= 1721 bytes.
+ 834 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3768
+ Installed-Size: 4824
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -660,49 +708,52 @@ bedtools_2.12.0-1_s390.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/bin/
--rwxr-xr-x root/root 142208 2011-06-09 22:29 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 175096 2011-06-09 22:29 ./usr/bin/coverageBed
--rwxr-xr-x root/root 106260 2011-06-09 22:29 ./usr/bin/linksBed
--rwxr-xr-x root/root 178328 2011-06-09 22:29 ./usr/bin/windowBed
--rwxr-xr-x root/root 114272 2011-06-09 22:29 ./usr/bin/subtractBed
--rwxr-xr-x root/root 113584 2011-06-09 22:29 ./usr/bin/flankBed
--rwxr-xr-x root/root 88372 2011-06-09 22:29 ./usr/bin/overlap
--rwxr-xr-x root/root 125312 2011-06-09 22:29 ./usr/bin/bamToBed
--rwxr-xr-x root/root 108592 2011-06-09 22:29 ./usr/bin/complementBed
--rwxr-xr-x root/root 190636 2011-06-09 22:29 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 110676 2011-06-09 22:29 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 142208 2011-06-09 22:29 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 65220 2011-06-09 22:29 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 260284 2011-06-09 22:29 ./usr/bin/pairToBed
--rwxr-xr-x root/root 134392 2011-06-09 22:29 ./usr/bin/bedToBam
--rwxr-xr-x root/root 96936 2011-06-09 22:29 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109616 2011-06-09 22:29 ./usr/bin/mergeBed
--rwxr-xr-x root/root 120888 2011-06-09 22:29 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 179692 2011-06-09 22:29 ./usr/bin/pairToPair
--rwxr-xr-x root/root 170776 2011-06-09 22:29 ./usr/bin/annotateBed
--rwxr-xr-x root/root 131016 2011-06-09 22:29 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 120876 2011-06-09 22:29 ./usr/bin/closestBed
--rwxr-xr-x root/root 194732 2011-06-09 22:29 ./usr/bin/intersectBed
--rwxr-xr-x root/root 202924 2011-06-09 22:29 ./usr/bin/fjoin
--rwxr-xr-x root/root 145864 2011-06-09 22:29 ./usr/bin/sortBed
--rwxr-xr-x root/root 105832 2011-06-09 22:29 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-09 22:27 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-09 22:29 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/bin/
+-rwxr-xr-x root/root 284936 2011-09-11 01:23 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 105300 2011-09-11 01:23 ./usr/bin/linksBed
+-rwxr-xr-x root/root 289320 2011-09-11 01:23 ./usr/bin/windowBed
+-rwxr-xr-x root/root 112776 2011-09-11 01:23 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 276760 2011-09-11 01:23 ./usr/bin/tagBam
+-rwxr-xr-x root/root 113232 2011-09-11 01:23 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88092 2011-09-11 01:23 ./usr/bin/overlap
+-rwxr-xr-x root/root 228656 2011-09-11 01:23 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 108584 2011-09-11 01:23 ./usr/bin/complementBed
+-rwxr-xr-x root/root 301340 2011-09-11 01:23 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 112712 2011-09-11 01:23 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 143496 2011-09-11 01:23 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63540 2011-09-11 01:23 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 370984 2011-09-11 01:23 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 231920 2011-09-11 01:23 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 96960 2011-09-11 01:23 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 108556 2011-09-11 01:23 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 120880 2011-09-11 01:23 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 176580 2011-09-11 01:23 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 104452 2011-09-11 01:23 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 130704 2011-09-11 01:23 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 143660 2011-09-11 01:23 ./usr/bin/nucBed
+-rwxr-xr-x root/root 120844 2011-09-11 01:23 ./usr/bin/closestBed
+-rwxr-xr-x root/root 305536 2011-09-11 01:23 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 305432 2011-09-11 01:23 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 145408 2011-09-11 01:23 ./usr/bin/sortBed
+-rwxr-xr-x root/root 105488 2011-09-11 01:23 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 01:21 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 01:23 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -716,7 +767,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-9d0daa96-45ed-4e50-8953-2eff183d5a08/build/buildd-bedtools_2.12.0-1-s390-3rG7yH
+Purging /var/lib/schroot/mount/sid-s390-sbuild-db1373a3-d9e1-481d-ab17-381d2076e7e2/build/buildd-bedtools_2.13.1-1-s390-h0Qq00
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -724,18 +775,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 81684
-Build-Time: 139
+Build-Space: 106176
+Build-Time: 155
Distribution: sid
-Install-Time: 17
-Job: bedtools_2.12.0-1
+Install-Time: 10
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 188
-Source-Version: 2.12.0-1
-Space: 81684
+Package-Time: 206
+Source-Version: 2.13.1-1
+Space: 106176
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110609-2229
-Build needed 00:03:08, 81684k disc space
-Signature with key '9BD94C88' requested:
+Finished at 20110911-0123
+Build needed 00:03:26, 106176k disc space
+Signature with key '2D941D26' requested:
diff --git a/sparc.log b/sparc.log
index f91615a..86031a7 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,69 @@
-From buildd at spontini.debian.org Thu Jun 09 02:39:16 2011
-Return-path: <buildd at spontini.debian.org>
+From buildd at lebrun.debian.org Sun Sep 11 03:48:04 2011
+Return-path: <buildd at lebrun.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
- id 1QUV9Q-0003Gr-Bz
- for logs at buildd.debian.org; Thu, 09 Jun 2011 02:39:16 +0000
-Received: from spontini.debian.org ([2607:f8f0:610:4000:a00:20ff:fea0:918b])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1R2b1Y-0005CT-EH
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 03:48:04 +0000
+Received: from lebrun.debian.org ([193.198.184.10])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=spontini.debian.org,
- EMAIL=hostmaster at spontini.debian.org (verified)
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
- id 1QUV9P-0002Rm-9B
- for logs at buildd.debian.org; Thu, 09 Jun 2011 02:39:15 +0000
-Received: from buildd by spontini.debian.org with local (Exim 4.72)
- (envelope-from <buildd at spontini.debian.org>)
- id 1QUV9L-0006Qa-Hd; Thu, 09 Jun 2011 02:39:11 +0000
-Message-Id: <E1QUV9L-0006Qa-Hd at spontini.debian.org>
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1R2b1X-0001gZ-H2
+ for logs at buildd.debian.org; Sun, 11 Sep 2011 03:48:03 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1R2b1V-0001Wz-NB; Sun, 11 Sep 2011 03:48:01 +0000
+Message-Id: <E1R2b1V-0001Wz-NB 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: Thu, 9 Jun 2011 02:39:11 +0000
-From: buildd on spontini <buildd at spontini.debian.org>
-To: logs at buildd.debian.org,buildd-admin at spontini.debian.org
-Subject: Log for successful build of bedtools_2.12.0-1 on sparc (dist=sid)
-Key-Id: 3B3DF88C
+Date: Sun, 11 Sep 2011 03:48:01 +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_2.13.1-1 on sparc (dist=sid)
+Key-Id: 632E3DB6
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on spontini.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.12.0-1 (sparc) 09 Jun 2011 02:20 ║
+║ bedtools 2.13.1-1 (sparc) 11 Sep 2011 03:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.12.0-1
-Source Version: 2.12.0-1
+Version: 2.13.1-1
+Source Version: 2.13.1-1
Architecture: sparc
-Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5289 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [5756 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5289 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [49.7 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [92.0 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main sparc Packages [7229 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib sparc Packages [54.0 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [49.7 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [92.0 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7229 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [54.0 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [57.4 kB]
+Get:5 http://incoming.debian.org Release.gpg [836 B]
+Get:6 http://incoming.debian.org Release [1604 B]
+Get:7 http://incoming.debian.org unstable/main Sources [5756 kB]
+Get:8 http://debian.carnet.hr unstable/non-free Sources [102 kB]
+Get:9 http://debian.carnet.hr unstable/main sparc Packages [7528 kB]
+Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.8 kB]
+Ign http://debian.carnet.hr unstable/contrib TranslationIndex
+Get:11 http://debian.carnet.hr unstable/main TranslationIndex [2045 B]
+Get:12 http://incoming.debian.org unstable/contrib Sources [57.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [102 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7528 kB]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:17 http://incoming.debian.org Sources [47.0 kB]
-Get:18 http://incoming.debian.org Packages [473 kB]
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [280 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 26.2 MB in 1min 6s (398 kB/s)
+Fetched 27.6 MB in 29s (928 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +84,11 @@ 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 796 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.12.0-1 (dsc) [1924 B]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.12.0-1 (tar) [790 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.12.0-1 (diff) [4198 B]
-Fetched 796 kB in 0s (3344 kB/s)
+Need to get 664 kB of source archives.
+Get:1 http://debian.carnet.hr/debian/ unstable/main bedtools 2.13.1-1 (dsc) [1921 B]
+Get:2 http://debian.carnet.hr/debian/ unstable/main bedtools 2.13.1-1 (tar) [658 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main bedtools 2.13.1-1 (diff) [4254 B]
+Fetched 664 kB in 0s (761 kB/s)
Download complete and in download only mode
Check arch
@@ -103,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.18-1)
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 19 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,39 +122,39 @@ Checking correctness of dependencies...
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, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22+b1)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b2)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-7)
+perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.7)
-sysvinit: already installed (2.88dsf-13.7)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-4)
-libc6-dev-sparc64: already installed (2.13-4)
-gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-20)
+libc6-dev-sparc64: already installed (2.13-20)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.6
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -177,51 +176,51 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 19 not upgraded.
-Need to get 9607 kB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-2 [35.9 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-1 [1013 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-3 [841 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
+Need to get 9525 kB of archives.
+After this operation, 29.3 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.08-1 [246 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main file sparc 5.08-1 [51.0 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9607 kB in 2s (4398 kB/s)
+Fetched 9525 kB in 8s (1143 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10977 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10815 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-2_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_sparc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.08-1_sparc.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_sparc.deb) ...
+Unpacking file (from .../archives/file_5.08-1_sparc.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -231,43 +230,43 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_sparc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_sparc.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
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 (1.21-6) ...
-Setting up libpipeline1 (1.2.0-2) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up libmagic1 (5.08-1) ...
+Setting up file (5.08-1) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -275,11 +274,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.51.20110523-1 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6-dev_2.13-4 libstdc++6_4.6.0-10 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.39-1
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.51.20110523-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.7 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libc6-dev-sparc64_2.13-4 libc6-sparc64_2.13-4 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-10 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-10 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-2 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libss2_1.41.12-4 libstdc++6_4.6.0-10 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7 perl-base_5.12.3-7 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.7 sysvinit_2.88dsf-13.7 sysvinit-utils_2.88dsf-13.7 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-20 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b2 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libc6-dev-sparc64_2.13-20 libc6-sparc64_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15+b1 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -290,12 +289,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jun 8 08:23:42 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sun Sep 11 00:44:52 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.12.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.12.0
-dpkg-source: info: unpacking bedtools_2.12.0.orig.tar.bz2
-dpkg-source: info: unpacking bedtools_2.12.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.1
+dpkg-source: info: unpacking bedtools_2.13.1.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -311,24 +310,24 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.12.0-1
- dpkg-source --before-build bedtools-2.12.0
+dpkg-buildpackage: source version 2.13.1-1
+ dpkg-source --before-build bedtools-2.13.1
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,22 +338,23 @@ rm -f debian/stamp-patch*
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1/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_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -368,11 +368,10 @@ Building BEDTools:
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-- Building in src/utils/tabFile
- * compiling tabFile.cpp
-
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
+genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+genomeFile.cpp:51:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- Building in src/utils/gzstream
g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
@@ -386,24 +385,74 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
* compiling BamReader.cpp
* compiling BamWriter.cpp
- * compiling BGZF.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
- * compiling BamIndex.cpp
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
+annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
* linking annotateBed
- Building in src/bamToBed
* compiling bamToBed.cpp
+bamToBed.cpp: In function 'int main(int, char**)':
+bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
* linking bamToBed
- Building in src/bedToBam
* compiling bedToBam.cpp
+bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
* linking bedToBam
- Building in src/bedToIgv
@@ -429,13 +478,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling coverageBed.cpp
* linking coverageBed
-- Building in src/cuffToTrans
- * compiling cuffToTransMain.cpp
- * compiling cuffToTrans.cpp
- * compiling Fasta.cpp
- * compiling split.cpp
- * linking cuffToTrans
-
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
@@ -446,11 +488,6 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling flankBed.cpp
* linking flankBed
-- Building in src/fjoin
- * compiling fjoinMain.cpp
- * compiling fjoin.cpp
- * linking fjoin
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
@@ -473,21 +510,49 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/mergeBed
* compiling mergeMain.cpp
+mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
* linking mergeBed
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
- Building in src/overlap
* compiling overlap.cpp
+overlap.cpp: In function 'int main(int, char**)':
+overlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
* linking overlap
- Building in src/pairToBed
* compiling pairToBedMain.cpp
+pairToBedMain.cpp: In function 'int main(int, char**)':
+pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
+pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
+pairToBed.cpp:254:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
+pairToBed.cpp:306:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
+pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToPair.cpp
+pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
+pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
+pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
* linking pairToPair
- Building in src/shuffleBed
@@ -507,12 +572,25 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/subtractBed
* compiling subtractMain.cpp
+subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
* linking subtractBed
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
+unionBedGraphsMain.cpp: In function 'int 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]
* linking unionBedGraphs
- Building in src/windowBed
@@ -520,7 +598,7 @@ g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU/bedtools-2.12.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM/bedtools-2.13.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -529,6 +607,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/bedtools.substvars
@@ -563,59 +642,64 @@ dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
-dh_builddeb -pbedtools
-dpkg-deb: building package `bedtools' in `../bedtools_2.12.0-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (spontini) <buildd_sparc-spontini at buildd.debian.org> >../bedtools_2.12.0-1_sparc.changes
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.1-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.13.1-1_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-2.12.0
+ dpkg-source --after-build bedtools-2.13.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110609-0238
+Build finished at 20110911-0347
-bedtools_2.12.0-1_sparc.changes:
+bedtools_2.13.1-1_sparc.changes:
Format: 1.8
-Date: Wed, 08 Jun 2011 17:01:19 +0900
+Date: Sat, 10 Sep 2011 23:32:43 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.12.0-1
+Version: 2.13.1-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (spontini) <buildd_sparc-spontini 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
-Closes: 629597
Changes:
- bedtools (2.12.0-1) unstable; urgency=low
+ bedtools (2.13.1-1) unstable; urgency=low
.
- * Initial release (Closes: #629597)
+ [2e3fe5e] New upstream release.
+ [ff5450e] Compress source and binary packages with xz.
+ [ef58a33] Suggest filo for the groupBy command.
+ [df206c0] Mangle debian/watch download URL.
+ [2fe7cff] Simplified repacking as upstream tarballs do not contain
+ ‘*/*DS_Store’ files anymore.
Checksums-Sha1:
- 873375cd0de121b66f403f3d7d80192e1f797abb 1406044 bedtools_2.12.0-1_sparc.deb
+ c37108b496bfa2ac562cb16fc863f10000259995 551098 bedtools_2.13.1-1_sparc.deb
Checksums-Sha256:
- 3a6555ede825633617973c396aef78acedb89f2019fdd6cfdb94ca3e5fcd5328 1406044 bedtools_2.12.0-1_sparc.deb
+ 67f99f0f8e7646abaeefeaed1a121b07924ddc4ae7942d82afe3441053b8c1c1 551098 bedtools_2.13.1-1_sparc.deb
Files:
- 508115a6b733070b696018d5e9197794 1406044 science optional bedtools_2.12.0-1_sparc.deb
+ 901158715531a96c6e820ec0b4e10adc 551098 science optional bedtools_2.13.1-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.12.0-1_sparc.deb
+bedtools_2.13.1-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 1406044 bytes: control archive= 1648 bytes.
- 761 bytes, 15 lines control
- 1978 bytes, 34 lines md5sums
+ size 551098 bytes: control archive= 1725 bytes.
+ 835 bytes, 18 lines control
+ 2028 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.12.0-1
+ Version: 2.13.1-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3404
+ Installed-Size: 4660
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
Section: science
Priority: optional
Homepage: http://code.google.com/p/bedtools/
@@ -625,49 +709,52 @@ bedtools_2.12.0-1_sparc.deb
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
BEDTools, one can develop sophisticated pipelines that answer complicated
research questions by streaming several BEDTools together.
-
-drwxr-xr-x root/root 0 2011-06-09 02:37 ./
-drwxr-xr-x root/root 0 2011-06-09 02:38 ./usr/
-drwxr-xr-x root/root 0 2011-06-09 02:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-06-09 02:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-06-09 02:38 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 4611 2011-06-08 07:59 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1586 2011-04-04 01:30 ./usr/share/doc/bedtools/README.rst.gz
--rw-r--r-- root/root 156 2011-06-08 08:01 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 8577 2011-04-04 01:30 ./usr/share/doc/bedtools/changelog.gz
-drwxr-xr-x root/root 0 2011-06-09 02:38 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-06-09 02:24 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-04-04 01:30 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-04-04 01:30 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-06-09 02:38 ./usr/bin/
--rwxr-xr-x root/root 106456 2011-06-09 02:38 ./usr/bin/sortBed
--rwxr-xr-x root/root 93000 2011-06-09 02:38 ./usr/bin/overlap
--rwxr-xr-x root/root 109412 2011-06-09 02:38 ./usr/bin/mergeBed
--rwxr-xr-x root/root 168424 2011-06-09 02:38 ./usr/bin/coverageBed
--rwxr-xr-x root/root 186120 2011-06-09 02:38 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 88412 2011-06-09 02:38 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 102060 2011-06-09 02:38 ./usr/bin/complementBed
--rwxr-xr-x root/root 200520 2011-06-09 02:38 ./usr/bin/pairToBed
--rwxr-xr-x root/root 95360 2011-06-09 02:38 ./usr/bin/subtractBed
--rwxr-xr-x root/root 103688 2011-06-09 02:38 ./usr/bin/flankBed
--rwxr-xr-x root/root 126504 2011-06-09 02:38 ./usr/bin/pairToPair
--rwxr-xr-x root/root 126892 2011-06-09 02:38 ./usr/bin/cuffToTrans
--rwxr-xr-x root/root 64284 2011-06-09 02:38 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 101256 2011-06-09 02:38 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 183512 2011-06-09 02:38 ./usr/bin/intersectBed
--rwxr-xr-x root/root 184096 2011-06-09 02:38 ./usr/bin/fjoin
--rwxr-xr-x root/root 103000 2011-06-09 02:38 ./usr/bin/closestBed
--rwxr-xr-x root/root 104520 2011-06-09 02:38 ./usr/bin/bamToBed
--rwxr-xr-x root/root 126892 2011-06-09 02:38 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 101224 2011-06-09 02:38 ./usr/bin/slopBed
--rwxr-xr-x root/root 113412 2011-06-09 02:38 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 109412 2011-06-09 02:38 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 167124 2011-06-09 02:38 ./usr/bin/annotateBed
--rwxr-xr-x root/root 101220 2011-06-09 02:38 ./usr/bin/linksBed
--rwxr-xr-x root/root 121860 2011-06-09 02:38 ./usr/bin/bedToBam
--rwxr-xr-x root/root 175304 2011-06-09 02:38 ./usr/bin/windowBed
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/bin/
+-rwxr-xr-x root/root 293428 2011-09-11 03:47 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 290196 2011-09-11 03:47 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 101748 2011-09-11 03:47 ./usr/bin/complementBed
+-rwxr-xr-x root/root 174864 2011-09-11 03:47 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 266364 2011-09-11 03:47 ./usr/bin/tagBam
+-rwxr-xr-x root/root 139124 2011-09-11 03:47 ./usr/bin/nucBed
+-rwxr-xr-x root/root 281968 2011-09-11 03:47 ./usr/bin/windowBed
+-rwxr-xr-x root/root 138584 2011-09-11 03:47 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 106980 2011-09-11 03:47 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 57444 2011-09-11 03:47 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 298368 2011-09-11 03:47 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 101124 2011-09-11 03:47 ./usr/bin/slopBed
+-rwxr-xr-x root/root 109240 2011-09-11 03:47 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 117456 2011-09-11 03:47 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105432 2011-09-11 03:47 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 117564 2011-09-11 03:47 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 358836 2011-09-11 03:47 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 93284 2011-09-11 03:47 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 125796 2011-09-11 03:47 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 103412 2011-09-11 03:47 ./usr/bin/linksBed
+-rwxr-xr-x root/root 84744 2011-09-11 03:47 ./usr/bin/overlap
+-rwxr-xr-x root/root 273920 2011-09-11 03:47 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 143084 2011-09-11 03:47 ./usr/bin/sortBed
+-rwxr-xr-x root/root 224264 2011-09-11 03:47 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101048 2011-09-11 03:47 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 109316 2011-09-11 03:47 ./usr/bin/flankBed
+-rwxr-xr-x root/root 224524 2011-09-11 03:47 ./usr/bin/bedToBam
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-09-11 03:38 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 586 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2011-09-07 00:36 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-09-07 00:36 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-11 03:47 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 4611 2011-09-10 14:21 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 10990 2011-09-07 00:36 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1586 2011-09-07 00:36 ./usr/share/doc/bedtools/README.rst.gz
+-rw-r--r-- root/root 391 2011-09-10 14:32 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -681,7 +768,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-6924978a-4237-4228-95c7-9be5dd0cbd10/build/buildd-bedtools_2.12.0-1-sparc-AgSgRU
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-5c95ad46-e4ab-466d-b350-feb701e4c93e/build/buildd-bedtools_2.13.1-1-sparc-UUAkMM
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -689,18 +776,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 57984
-Build-Time: 857
+Build-Space: 99016
+Build-Time: 581
Distribution: sid
-Install-Time: 124
-Job: bedtools_2.12.0-1
+Install-Time: 63
+Job: bedtools_2.13.1-1
Package: bedtools
-Package-Time: 1097
-Source-Version: 2.12.0-1
-Space: 57984
+Package-Time: 695
+Source-Version: 2.13.1-1
+Space: 99016
Status: successful
-Version: 2.12.0-1
+Version: 2.13.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110609-0238
-Build needed 00:18:17, 57984k disc space
-Signature with key '3B3DF88C' requested:
+Finished at 20110911-0347
+Build needed 00:11:35, 99016k disc space
+Signature with key '632E3DB6' requested:
--
Suite of utilities for comparing genomic features.
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