[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.14.3-1-2-g952b00b
Charles Plessy
plessy at debian.org
Wed Jan 11 14:23:42 UTC 2012
The following commit has been merged in the meta branch:
commit 952b00b45c60a65da87fbfdb5e048a7a613da992
Author: Charles Plessy <plessy at debian.org>
Date: Wed Jan 11 23:23:37 2012 +0900
Build logs for 2.15.0-1.
diff --git a/armel.log b/armel.log
index 1636a80..b73438f 100644
--- a/armel.log
+++ b/armel.log
@@ -1,67 +1,68 @@
-From buildd at alwyn.debian.org Sat Nov 05 02:20:58 2011
-Return-path: <buildd at alwyn.debian.org>
+From buildd at antheil.debian.org Wed Jan 11 08:54:50 2012
+Return-path: <buildd at antheil.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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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 alwyn.debian.org>)
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-Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
+ (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
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+ for logs at buildd.debian.org; Wed, 11 Jan 2012 08:54:50 +0000
+Received: from antheil.islands.arm.com ([217.140.96.60]
+ helo=antheil.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
+ CN=antheil.debian.org, EMAIL=hostmaster at antheil.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
- id 1RMVsP-0001S5-0K
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-Date: Sat, 05 Nov 2011 02:20:55 +0000
-Message-Id: <E1RMVsN-0000a1-DH at alwyn.debian.org>
-From: buildd on alwyn <buildd at alwyn.debian.org>
-To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on armel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
+ id 1RktxH-0007pJ-29
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+Date: Wed, 11 Jan 2012 08:54:45 +0000
+Message-Id: <E1RktxF-0007bA-NC at antheil.debian.org>
+From: buildd on antheil <buildd at antheil.debian.org>
+To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.15.0-1 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 alwyn.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (armel) 05 Nov 2011 01:53 ║
+║ bedtools 2.15.0-1 (armel) 11 Jan 2012 08:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: armel
-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 [5890 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6000 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 [5890 kB]
-Get:7 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
-Get:8 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
-Get:9 http://ftp.uk.debian.org unstable/main armel Packages [7651 kB]
-Get:10 http://ftp.uk.debian.org unstable/contrib armel Packages [55.2 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [100 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [7786 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:11 http://incoming.debian.org unstable/main armel Packages [7786 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [55.0 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:11 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2085 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:14 http://incoming.debian.org unstable/main armel Packages [7651 kB]
-Get:15 http://incoming.debian.org unstable/contrib armel Packages [55.2 kB]
+Get:14 http://incoming.debian.org unstable/contrib armel Packages [55.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
-Ign http://incoming.debian.org Translation-en
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [586 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.1 MB in 1min 4s (437 kB/s)
+Ign http://incoming.debian.org Translation-en
+Fetched 29.0 MB in 1min 6s (439 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +83,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (797 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (784 kB/s)
Download complete and in download only mode
Check arch
@@ -100,132 +101,171 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 24 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
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 (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.08)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-3)
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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 25 not upgraded.
-Need to get 9379 kB of archives.
-After this operation, 26.3 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-4 [34.0 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 libglib2.0-0 armel 2.28.8-1 [1552 kB]
-Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-5 [815 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-2 [110 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.09-2 [247 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.09-2 [51.8 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 24 not upgraded.
+Need to get 16.6 MB of archives.
+After this operation, 46.0 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armel 5.9-4 [303 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-5 [34.2 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armel 1.0.0e-3 [1010 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.30.2-4 [1742 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-5.1 [814 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-2 [110 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armel 2.0.1-7.2 [114 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armel 4.8.30-11 [622 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-3 [987 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.09-2 [247 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.09-2 [51.8 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armel 3.7.9-3 [395 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armel 2.7.2-9 [1584 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armel 2.7.2-9 [2597 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-2 [28.5 kB]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 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
-Fetched 9379 kB in 1s (8558 kB/s)
+Fetched 16.6 MB in 4s (3461 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10565 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_armel.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10465 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_armel.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armel.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_armel.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_armel.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_armel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_armel.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_armel.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armel.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_armel.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armel.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_armel.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_armel.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_armel.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_armel.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_armel.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-3_armel.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_armel.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-9_armel.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously unselected package gettext.
@@ -233,49 +273,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_armel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_armel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-3) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-16 gcc-4.6_4.6.1-16 libc6-dev_2.13-21 libstdc++6_4.6.1-16 libstdc++6-4.6-dev_4.6.1-16 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-16 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-16 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-16 gcc-4.6-base_4.6.1-16 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-16 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.1-16 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.1-16 libstdc++6-4.6-dev_4.6.1-16 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-2 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-2 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-2 g++-4.6_4.6.2-9 gcc_4:4.6.2-2 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.08 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.19.1-5 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-9 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -286,12 +338,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,24 +354,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -332,21 +384,21 @@ 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_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -379,41 +431,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -433,176 +494,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -641,90 +698,67 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
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/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/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/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/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/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/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/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/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/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/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/complementBed 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/multiIntersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org> >../bedtools_2.14.3-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../bedtools_2.15.0-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0220
+Build finished at 20120111-0854
-bedtools_2.14.3-1_armel.changes:
+bedtools_2.15.0-1_armel.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org>
+Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 9ac81c842053d4d71d6a139b7d604afa8468e6d8 554080 bedtools_2.14.3-1_armel.deb
+ e6e1417713a2d3faab139338fdd43a86b0b2828e 333406 bedtools_2.15.0-1_armel.deb
Checksums-Sha256:
- b08774de3589fa3df41164ead694830e422f5b5cfe7e59c6aa9a12c71df6975b 554080 bedtools_2.14.3-1_armel.deb
+ 47d37c342c7df5e01ac02af7c01390e884fbe2c2092ea8b9cbd05a8c81af4965 333406 bedtools_2.15.0-1_armel.deb
Files:
- ad26a27042d35a0adce1ab6db83580e4 554080 science optional bedtools_2.14.3-1_armel.deb
+ 30a6b0459b3d6b804a38a2fc3fde6f7d 333406 science optional bedtools_2.15.0-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_armel.deb
+bedtools_2.15.0-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 554080 bytes: control archive= 1759 bytes.
+ size 333406 bytes: control archive= 1869 bytes.
865 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4067
+ Installed-Size: 1092
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -740,50 +774,54 @@ bedtools_2.14.3-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/bin/
--rwxr-xr-x root/root 92284 2011-11-05 02:19 ./usr/bin/annotateBed
--rwxr-xr-x root/root 127640 2011-11-05 02:19 ./usr/bin/sortBed
--rwxr-xr-x root/root 88208 2011-11-05 02:19 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 231848 2011-11-05 02:19 ./usr/bin/windowBed
--rwxr-xr-x root/root 112836 2011-11-05 02:19 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 92316 2011-11-05 02:19 ./usr/bin/complementBed
--rwxr-xr-x root/root 92300 2011-11-05 02:19 ./usr/bin/linksBed
--rwxr-xr-x root/root 75920 2011-11-05 02:19 ./usr/bin/overlap
--rwxr-xr-x root/root 305600 2011-11-05 02:19 ./usr/bin/pairToBed
--rwxr-xr-x root/root 122308 2011-11-05 02:19 ./usr/bin/nucBed
--rwxr-xr-x root/root 121824 2011-11-05 02:19 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 102332 2011-11-05 02:19 ./usr/bin/flankBed
--rwxr-xr-x root/root 108672 2011-11-05 02:19 ./usr/bin/closestBed
--rwxr-xr-x root/root 93804 2011-11-05 02:19 ./usr/bin/mergeBed
--rwxr-xr-x root/root 289208 2011-11-05 02:19 ./usr/bin/intersectBed
--rwxr-xr-x root/root 240020 2011-11-05 02:19 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 104612 2011-11-05 02:19 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 223664 2011-11-05 02:19 ./usr/bin/tagBam
--rwxr-xr-x root/root 159572 2011-11-05 02:19 ./usr/bin/pairToPair
--rwxr-xr-x root/root 186644 2011-11-05 02:19 ./usr/bin/bamToBed
--rwxr-xr-x root/root 122084 2011-11-05 02:19 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 231824 2011-11-05 02:19 ./usr/bin/coverageBed
--rwxr-xr-x root/root 240604 2011-11-05 02:19 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 104576 2011-11-05 02:19 ./usr/bin/subtractBed
--rwxr-xr-x root/root 186804 2011-11-05 02:19 ./usr/bin/bedToBam
--rwxr-xr-x root/root 55956 2011-11-05 02:19 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 94764 2011-11-05 02:19 ./usr/bin/slopBed
--rwxr-xr-x root/root 96440 2011-11-05 02:19 ./usr/bin/maskFastaFromBed
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/bin/
+-rwxr-xr-x root/root 32 2012-01-11 08:53 ./usr/bin/closestBed
+-rwxr-xr-x root/root 34 2012-01-11 08:53 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-01-11 08:53 ./usr/bin/sortBed
+-rwxr-xr-x root/root 30 2012-01-11 08:53 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 36 2012-01-11 08:53 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 29 2012-01-11 08:53 ./usr/bin/slopBed
+-rwxr-xr-x root/root 32 2012-01-11 08:53 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 30 2012-01-11 08:53 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-01-11 08:53 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 1056896 2012-01-11 08:54 ./usr/bin/bedtools
+-rwxr-xr-x root/root 30 2012-01-11 08:53 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-01-11 08:53 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 28 2012-01-11 08:53 ./usr/bin/tagBam
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 34 2012-01-11 08:53 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 31 2012-01-11 08:53 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 34 2012-01-11 08:53 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 32 2012-01-11 08:53 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-01-11 08:53 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-01-11 08:53 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 35 2012-01-11 08:53 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-01-11 08:53 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 32 2012-01-11 08:53 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 34 2012-01-11 08:53 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 35 2012-01-11 08:53 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-01-11 08:53 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 28 2012-01-11 08:53 ./usr/bin/nucBed
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 08:31 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 08:54 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -797,7 +835,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-94c973b7-9831-421b-bfce-1b1012141207/build/buildd-bedtools_2.14.3-1-armel-yq6poG
+Purging /var/lib/schroot/mount/sid-armel-sbuild-60302bc7-fb58-4465-91b9-d135480d3f69/build/buildd-bedtools_2.15.0-1-armel-XxZntt
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -805,19 +843,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 100308
-Build-Time: 1451
+Build-Space: 65992
+Build-Time: 1374
Distribution: sid
-Install-Time: 90
-Job: bedtools_2.14.3-1
+Install-Time: 142
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1636
-Source-Version: 2.14.3-1
-Space: 100308
+Package-Time: 1615
+Source-Version: 2.15.0-1
+Space: 65992
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0220
-Build needed 00:27:16, 100308k disc space
-Signature with key 'E832C355' requested:
+Finished at 20120111-0854
+Build needed 00:26:55, 65992k disc space
+Signature with key '5EAEB276' requested:
diff --git a/armhf.log b/armhf.log
index 76f7413..b50b33f 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,67 +1,67 @@
-From buildd at hoiby.debian.org Mon Nov 28 19:37:56 2011
-Return-path: <buildd at hoiby.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at hummel.debian.org Wed Jan 11 07:33:42 2012
+Return-path: <buildd at hummel.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at hoiby.debian.org>)
- id 1RV71Y-00014r-6X
- for logs at buildd.debian.org; Mon, 28 Nov 2011 19:37:56 +0000
-Received: from [217.140.96.71] (helo=hoiby.debian.org)
+ (Exim 4.72) (envelope-from <buildd at hummel.debian.org>)
+ id 1Rksgn-0002f9-W1
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:33:42 +0000
+Received: from hummel.ynic.york.ac.uk ([144.32.168.76] helo=hummel.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=hoiby.debian.org, EMAIL=hostmaster at hoiby.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at hoiby.debian.org>)
- id 1RV71X-0006Vx-9w
- for logs at buildd.debian.org; Mon, 28 Nov 2011 19:37:55 +0000
-Received: from buildd by hoiby.debian.org with local (Exim 4.77)
- (envelope-from <buildd at hoiby.debian.org>)
- id 1RV71V-0001GS-HJ; Mon, 28 Nov 2011 19:37:53 +0000
-From: buildd on hoiby <buildd at hoiby.debian.org>
-To: logs at buildd.debian.org,buildd-porters at hoiby.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on armhf (dist=sid)
+ CN=hummel.debian.org, EMAIL=hostmaster at hummel.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at hummel.debian.org>)
+ id 1Rksgn-0001eP-2K
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:33:41 +0000
+Received: from buildd by hummel.debian.org with local (Exim 4.77)
+ (envelope-from <buildd at hummel.debian.org>)
+ id 1Rksgk-0000DM-St; Wed, 11 Jan 2012 07:33:38 +0000
+From: buildd on hummel <buildd at hummel.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hummel.debian.org
+Subject: Log for successful build of bedtools_2.15.0-1 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RV71V-0001GS-HJ at hoiby.debian.org>
-Date: Mon, 28 Nov 2011 19:37:53 +0000
+Message-Id: <E1Rksgk-0000DM-St at hummel.debian.org>
+Date: Wed, 11 Jan 2012 07:33:38 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hoiby.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hummel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (armhf) 28 Nov 2011 19:15 ║
+║ bedtools 2.15.0-1 (armhf) 11 Jan 2012 07:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: armhf
-Get:1 http://ftp.debian.org unstable InRelease [181 kB]
-Get:2 http://incoming.debian.org unstable InRelease [181 kB]
-Get:3 http://ftp.debian.org unstable/main Sources [5911 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6000 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 [5911 kB]
-Get:6 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:7 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://incoming.debian.org unstable/main armhf Packages [4552 kB]
-Get:9 http://ftp.debian.org unstable/contrib Sources [56.5 kB]
-Get:10 http://ftp.debian.org unstable/non-free Sources [103 kB]
-Get:11 http://ftp.debian.org unstable/main armhf Packages [4552 kB]
-Get:12 http://incoming.debian.org unstable/contrib armhf Packages [33.7 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [100 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [7351 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [51.5 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2085 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main armhf Packages [7351 kB]
+Get:14 http://incoming.debian.org unstable/contrib armhf Packages [51.5 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 [1616 B]
-Get:15 http://incoming.debian.org Sources [36.7 kB]
-Get:16 http://incoming.debian.org Packages [1092 kB]
-Get:17 http://ftp.debian.org unstable/contrib armhf Packages [33.7 kB]
-Ign http://ftp.debian.org unstable/contrib TranslationIndex
-Get:18 http://ftp.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.debian.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 22.8 MB in 57s (397 kB/s)
+Fetched 28.1 MB in 1min 16s (367 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 928 kB of source archives.
-Get:1 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (1514 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (629 kB/s)
Download complete and in download only mode
Check arch
@@ -99,163 +99,210 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.2-1)
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 2 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 2 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1+b1)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.11
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 1 not upgraded.
-Need to get 9352 kB of archives.
-After this operation, 24.3 MB of additional disk space will be used.
-Get:1 http://ftp.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.0-5 [32.1 kB]
-Get:2 http://ftp.debian.org/debian/ unstable/main libpcre3 armhf 8.12-4 [222 kB]
-Get:3 http://ftp.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3 [22.2 kB]
-Get:4 http://ftp.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.30.2-4 [1672 kB]
-Get:5 http://ftp.debian.org/debian/ unstable/main libxml2 armhf 2.7.8.dfsg-5 [775 kB]
-Get:6 http://ftp.debian.org/debian/ unstable/main libcroco3 armhf 0.6.2-2 [104 kB]
-Get:7 http://ftp.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5 [404 kB]
-Get:8 http://ftp.debian.org/debian/ unstable/main bsdmainutils armhf 8.2.3 [201 kB]
-Get:9 http://ftp.debian.org/debian/ unstable/main groff-base armhf 1.21-6 [1029 kB]
-Get:10 http://ftp.debian.org/debian/ unstable/main man-db armhf 2.6.0.2-3 [976 kB]
-Get:11 http://ftp.debian.org/debian/ unstable/main libmagic1 armhf 5.09-2 [244 kB]
-Get:12 http://ftp.debian.org/debian/ unstable/main file armhf 5.09-2 [51.6 kB]
-Get:13 http://ftp.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-5 [131 kB]
-Get:14 http://ftp.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15 [97.2 kB]
-Get:16 http://ftp.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-5 [1925 kB]
-Get:17 http://ftp.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp.debian.org/debian/ unstable/main debhelper all 8.9.11 [552 kB]
-Get:20 http://ftp.debian.org/debian/ unstable/main diffstat armhf 1.54-1 [26.4 kB]
-Get:21 http://ftp.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:22 http://ftp.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.3.4.dfsg-3 [200 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 2 not upgraded.
+Need to get 16.1 MB of archives.
+After this operation, 41.5 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armhf 5.9-4+b1 [293 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.0-5+b1 [32.4 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armhf 1.0.0e-3 [959 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 8.12-4+b1 [222 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.30.2-4+b1 [1674 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.7.8.dfsg-5.1 [776 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.2-2+b1 [104 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armhf 2.0.1-7.2+b1 [106 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armhf 4.8.30-11 [590 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 8.2.3+b1 [201 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-6+b1 [1027 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.0.2-3+b1 [964 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.09-2+b1 [245 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.09-2+b1 [51.7 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-5+b1 [132 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armhf 3.7.9-2+b1 [366 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armhf 2.7.2-9 [1519 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armhf 2.7.2-9 [2551 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-5+b1 [1920 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-2 [27.4 kB]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.3.4.dfsg-3+b1 [187 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9352 kB in 2s (4360 kB/s)
+Fetched 16.1 MB in 2s (6458 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10684 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_armhf.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10692 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armhf.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_armhf.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_armhf.deb) ...
Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_armhf.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_armhf.deb) ...
Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_armhf.deb) ...
+Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_armhf.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_armhf.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_armhf.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_armhf.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armhf.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_armhf.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2+b1_armhf.deb) ...
Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armhf.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armhf.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3+b1_armhf.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_armhf.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6+b1_armhf.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_armhf.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3+b1_armhf.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_armhf.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_armhf.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_armhf.deb) ...
+Unpacking file (from .../file_5.09-2+b1_armhf.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_armhf.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_armhf.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2+b1_armhf.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_armhf.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-9_armhf.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ...
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_armhf.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5+b1_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_armhf.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armhf.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_armhf.deb) ...
+Setting up libncursesw5 (5.9-4+b1) ...
+Setting up libpipeline1 (1.2.0-5+b1) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpcre3 (8.12-4+b1) ...
+Setting up libffi5 (3.0.10-3+b1) ...
+Setting up libglib2.0-0 (2.30.2-4+b1) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
-Setting up libcroco3 (0.6.2-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
+Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libexpat1 (2.0.1-7.2+b1) ...
+Setting up libunistring0 (0.9.3-5+b1) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up bsdmainutils (8.2.3+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up groff-base (1.21-6+b1) ...
+Setting up man-db (2.6.0.2-3+b1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
-Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up libmagic1 (5.09-2+b1) ...
+Setting up file (5.09-2+b1) ...
+Setting up gettext-base (0.18.1.1-5+b1) ...
+Setting up libsqlite3-0 (3.7.9-2+b1) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up gettext (0.18.1.1-5+b1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.11) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
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 2 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.3 armhf (armv7l)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.1.1-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.2-1 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.2-1 g++-4.6_4.6.2-4 gcc_4:4.6.2-1 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 3.1.0-1-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3+b1 bsdutils_1:2.20.1-1.1 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2+b1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-10 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.09 html2text_1.3.2a-15+b1 initscripts_2.88dsf-18 insserv_1.14.0-2.1+b1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2+b1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2+b1 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-4+b1 libgmp10_2:5.0.2+dfsg-2+b1 libgomp1_4.6.2-11 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.09-2+b1 libmount1_2.20.1-1.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-6+b1 libpam-modules-bin_1.1.3-6+b1 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6+b1 libpcre3_8.12-4+b1 libpipeline1_1.2.0-5+b1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2+b1 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3+b1 lsb-base_3.2-28 make_3.81-8.1+b1 man-db_2.6.0.2-3+b1 mawk_1.3.3-16+b1 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.4.2+svn3283-3+b1 patch_2.6.1-2+b1 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p1-2+b1 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.3.4.dfsg-3+b1 zlib1g-dev_1:1.2.3.4.dfsg-3+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -266,12 +313,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -282,24 +329,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -312,21 +359,21 @@ 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_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -359,41 +406,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -413,176 +469,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -621,90 +673,67 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
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/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/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/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/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/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/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/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/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/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/complementBed 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/multiIntersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hoiby) <buildd_armhf-hoiby at buildd.debian.org> >../bedtools_2.14.3-1_armhf.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org> >../bedtools_2.15.0-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111128-1937
+Build finished at 20120111-0733
-bedtools_2.14.3-1_armhf.changes:
+bedtools_2.15.0-1_armhf.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: armhf
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (hoiby) <buildd_armhf-hoiby at buildd.debian.org>
+Maintainer: armhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 1f26b8312bb54a1a9895c6f948defaf425086de8 570276 bedtools_2.14.3-1_armhf.deb
+ c7c8799c8d9a457b5588b51a3dd9bc5e90937b1b 349698 bedtools_2.15.0-1_armhf.deb
Checksums-Sha256:
- 24f1084eb220f71538a0b5d4ae21acb9eed29ec9402de0514a541b0d60f02a1b 570276 bedtools_2.14.3-1_armhf.deb
+ 74283e6a92accd13bd7127ababb8e10a5641c8783a1021ed680479810e1d02e2 349698 bedtools_2.15.0-1_armhf.deb
Files:
- 7fcda3bf8e157d83110453bdb9dd6b81 570276 science optional bedtools_2.14.3-1_armhf.deb
+ 56e0c970edd89cd763a8bed32fdc6782 349698 science optional bedtools_2.15.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_armhf.deb
+bedtools_2.15.0-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 570276 bytes: control archive= 1760 bytes.
- 865 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ size 349698 bytes: control archive= 1866 bytes.
+ 864 bytes, 19 lines control
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 2966
+ Installed-Size: 871
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -720,50 +749,54 @@ bedtools_2.14.3-1_armhf.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/bin/
--rwxr-xr-x root/root 178576 2011-11-28 19:37 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 77380 2011-11-28 19:37 ./usr/bin/closestBed
--rwxr-xr-x root/root 166664 2011-11-28 19:37 ./usr/bin/coverageBed
--rwxr-xr-x root/root 117460 2011-11-28 19:37 ./usr/bin/pairToPair
--rwxr-xr-x root/root 65428 2011-11-28 19:37 ./usr/bin/complementBed
--rwxr-xr-x root/root 68044 2011-11-28 19:37 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 65272 2011-11-28 19:37 ./usr/bin/linksBed
--rwxr-xr-x root/root 137552 2011-11-28 19:37 ./usr/bin/bedToBam
--rwxr-xr-x root/root 43308 2011-11-28 19:37 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 89672 2011-11-28 19:37 ./usr/bin/nucBed
--rwxr-xr-x root/root 65132 2011-11-28 19:37 ./usr/bin/annotateBed
--rwxr-xr-x root/root 137508 2011-11-28 19:37 ./usr/bin/bamToBed
--rwxr-xr-x root/root 211344 2011-11-28 19:37 ./usr/bin/intersectBed
--rwxr-xr-x root/root 92260 2011-11-28 19:37 ./usr/bin/sortBed
--rwxr-xr-x root/root 53396 2011-11-28 19:37 ./usr/bin/overlap
--rwxr-xr-x root/root 75880 2011-11-28 19:37 ./usr/bin/subtractBed
--rwxr-xr-x root/root 67864 2011-11-28 19:37 ./usr/bin/slopBed
--rwxr-xr-x root/root 62032 2011-11-28 19:37 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 73180 2011-11-28 19:37 ./usr/bin/flankBed
--rwxr-xr-x root/root 88244 2011-11-28 19:37 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 167468 2011-11-28 19:37 ./usr/bin/windowBed
--rwxr-xr-x root/root 89108 2011-11-28 19:37 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 174468 2011-11-28 19:37 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 162188 2011-11-28 19:37 ./usr/bin/tagBam
--rwxr-xr-x root/root 223900 2011-11-28 19:37 ./usr/bin/pairToBed
--rwxr-xr-x root/root 75924 2011-11-28 19:37 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 67696 2011-11-28 19:37 ./usr/bin/mergeBed
--rwxr-xr-x root/root 80140 2011-11-28 19:37 ./usr/bin/shuffleBed
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-28 19:17 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/bin/
+-rwxr-xr-x root/root 30 2012-01-11 07:32 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 34 2012-01-11 07:32 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 34 2012-01-11 07:32 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 34 2012-01-11 07:32 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 07:32 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 32 2012-01-11 07:32 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 36 2012-01-11 07:32 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 28 2012-01-11 07:32 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-01-11 07:32 ./usr/bin/linksBed
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 32 2012-01-11 07:32 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:32 ./usr/bin/flankBed
+-rwxr-xr-x root/root 29 2012-01-11 07:32 ./usr/bin/slopBed
+-rwxr-xr-x root/root 28 2012-01-11 07:32 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 32 2012-01-11 07:32 ./usr/bin/closestBed
+-rwxr-xr-x root/root 831256 2012-01-11 07:33 ./usr/bin/bedtools
+-rwxr-xr-x root/root 34 2012-01-11 07:32 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:32 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 35 2012-01-11 07:32 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 28 2012-01-11 07:32 ./usr/bin/nucBed
+-rwxr-xr-x root/root 35 2012-01-11 07:32 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 35 2012-01-11 07:32 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 31 2012-01-11 07:32 ./usr/bin/windowBed
+-rwxr-xr-x root/root 35 2012-01-11 07:32 ./usr/bin/complementBed
+-rwxr-xr-x root/root 29 2012-01-11 07:32 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-01-11 07:32 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 36 2012-01-11 07:32 ./usr/bin/bed12ToBed6
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:13 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,7 +810,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-9447f43e-bdd4-452f-b900-d5db504db0ef/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-93040c22-317b-4469-a310-c75a2deb431f/build/buildd-bedtools_2.15.0-1-armhf-CNb06x
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -785,19 +818,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 98576
-Build-Time: 1201
+Build-Space: 66004
+Build-Time: 1195
Distribution: sid
-Install-Time: 61
-Job: bedtools_2.14.3-1
+Install-Time: 128
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1346
-Source-Version: 2.14.3-1
-Space: 98576
+Package-Time: 1428
+Source-Version: 2.15.0-1
+Space: 66004
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111128-1937
-Build needed 00:22:26, 98576k disc space
-Signature with key '49088707' requested:
+Finished at 20120111-0733
+Build needed 00:23:48, 66004k disc space
diff --git a/hurd-i386.log b/hurd-i386.log
index d89c9cf..5efdc49 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,74 +1,68 @@
-From buildd at rossini.debian.net Sat Nov 05 11:59:02 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+From buildd at ironforge.sceen.net Wed Jan 11 07:24:32 2012
+Return-path: <buildd at ironforge.sceen.net>
+Received: from ironforge.sceen.net ([46.105.42.111])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1RMetp-0005vK-Dy
- for logs at buildd.debian.org; Sat, 05 Nov 2011 11:59:02 +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 1RMetj-000JFM-Ty; Sat, 05 Nov 2011 12:58:56 +0100
-Received: from buildd by rossini.debian.net with local (Exim 4.72)
- (envelope-from <buildd at rossini.debian.net>)
- id 1RMeti-0001HI-34; Sat, 05 Nov 2011 11:58:54 +0000
-Date: Sat, 05 Nov 2011 11:58:54 +0000
-Message-Id: <E1RMeti-0001HI-34 at rossini.debian.net>
-From: Build Daemon <buildd at rossini.debian.net>
-To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
- logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on hurd-i386 (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
+ id 1RksXw-0000rO-8g
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:24:32 +0000
+Received: from buildd by ironforge.sceen.net with local (Exim 4.77)
+ (envelope-from <buildd at ironforge.sceen.net>)
+ id 1RksXu-0006VQ-CG; Wed, 11 Jan 2012 08:24:30 +0100
+From: Build Daemon <buildd at ironforge.sceen.net>
+To: samuel.thibault at ens-lyon.org,mbanck at gmx.net,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.15.0-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RksXu-0006VQ-CG at ironforge.sceen.net>
+Date: Wed, 11 Jan 2012 08:24:30 +0100
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rossini.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (hurd-i386) 05 Nov 2011 11:39 ║
+║ bedtools 2.15.0-1 (hurd-i386) 11 Jan 2012 08:18 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: hurd-i386
-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
-Hit http://ftp.fr.debian.org unstable InRelease
-Hit http://ftp.fr.debian.org experimental InRelease
+Hit http://ftp.fr.debian.org sid InRelease
+Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
+Get:1 ftp://ftp.debian-ports.org unreleased InRelease
+Ign ftp://ftp.debian-ports.org unreleased InRelease
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Ign http://ftp.debian-ports.org unreleased InRelease
-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.fr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.fr.debian.org sid/main TranslationIndex
+Hit ftp://ftp.debian-ports.org unreleased Release.gpg
+Hit http://incoming.debian.org Release.gpg
+Ign http://ftp.fr.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit ftp://ftp.debian-ports.org unreleased Release
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
Hit http://incoming.debian.org Release
-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
-Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Hit ftp://ftp.debian-ports.org unreleased/main hurd-i386 Packages
Hit http://incoming.debian.org Sources
-Hit http://ftp.fr.debian.org unstable/main TranslationIndex
-Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
Hit http://incoming.debian.org Packages
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Get:2 ftp://ftp.debian-ports.org unreleased/main TranslationIndex
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Fetched 836 B in 2min 50s (5 B/s)
+Ign ftp://ftp.debian-ports.org unreleased/main TranslationIndex
+Get:3 ftp://ftp.debian-ports.org unreleased/main Translation-en
+Get:4 ftp://ftp.debian-ports.org unreleased/main Translation-en
+Get:5 ftp://ftp.debian-ports.org unreleased/main Translation-en
+Get:6 ftp://ftp.debian-ports.org unreleased/main Translation-en
+Ign ftp://ftp.debian-ports.org unreleased/main Translation-en
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,11 +83,11 @@ 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 928 kB of source archives.
-Get:1 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (1742 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 3s (283 kB/s)
Download complete and in download only mode
Check arch
@@ -107,31 +101,33 @@ 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 (1.18.1-1+hurd.1)
Checking for dependency conflicts...
Installing positive 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:
+ groff-base libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Removing negative 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:
+ groff-base libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -139,81 +135,95 @@ bash: already installed (4.1-3+hurd.1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.3.12-9)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-hurd: already installed (20110519-3)
-ncurses-base: already installed (5.9-2)
+hurd: already installed (20111106-1)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-4)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
-libc0.3-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+libc0.3-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
-hurd-dev: already installed (20110519-3)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+hurd-dev: already installed (20111106-1)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
-zlib1g-dev: missing
+python: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python
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:
+ libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
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
+ libdb4.8 libexpat1 libmagic1 libsqlite3-0 libunistring0 mime-support
+ po-debconf python-minimal python2.7 python2.7-minimal
Suggested packages:
- devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc libmail-box-perl python-doc python-tk
+ python2.7-doc binfmt-support procmail graphviz default-mta
+ mail-transport-agent
Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libmail-sendmail-perl
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 21 not upgraded.
-Need to get 0 B/7203 kB of archives.
-After this operation, 20.4 MB of additional disk space will be used.
+ libcroco3 libdb4.8 libexpat1 libmagic1 libsqlite3-0 libunistring0
+ mime-support po-debconf python python-minimal python2.7 python2.7-minimal
+ quilt
+0 upgraded, 21 newly installed, 0 to remove and 28 not upgraded.
+Need to get 0 B/10.3 MB of archives.
+After this operation, 32.2 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- libglib2.0-0 libxml2 libcroco3 libexpat1 libunistring0 libmagic1 file
- gettext-base cdbs html2text gettext intltool-debian po-debconf debhelper
- diffstat quilt zlib1g-dev
+ libcroco3 libexpat1 libunistring0 libdb4.8 libmagic1 file gettext-base
+ libsqlite3-0 mime-support python2.7-minimal python2.7 python-minimal python
+ cdbs html2text gettext intltool-debian po-debconf debhelper diffstat quilt
Authentication warning overridden.
-Selecting previously unselected package libglib2.0-0.
-(Reading database ... 12466 files and directories currently installed.)
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_hurd-i386.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_hurd-i386.deb) ...
Selecting previously unselected package libcroco3.
+(Reading database ... 13654 files and directories currently installed.)
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_hurd-i386.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_hurd-i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_hurd-i386.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_hurd-i386.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_hurd-i386.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.09-2_hurd-i386.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_hurd-i386.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-3_hurd-i386.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_hurd-i386.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-9_hurd-i386.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
Selecting previously unselected package gettext.
@@ -221,47 +231,48 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_hurd-i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_hurd-i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
-Setting up libglib2.0-0 (2.28.8-1) ...
-No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-3) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15+b1) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Removing negative 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:
+ libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 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_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.4_4.4.6-11 cpp-4.5_4.5.3-9 cpp-4.6_4.6.1-9+hurd.1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.15.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-11 gcc-4.4-base_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.4_4.4.6-11 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-11 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 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 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_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.42.0_1.42.0-4+b3 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libexpat1_2.0.1-7.2 libfribidi0_0.19.2-1 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_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libident_0.22-3 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-9 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 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_6.2-7 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-08-10-1 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_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 wget_1.13-1 whiptail_0.52.11-2.1 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-2+hurd.1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5+hurd.1 gcc-4.6_4.6.2-5+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20111106-1 libc0.3-dev_2.13-24 libstdc++6_4.6.2-5+hurd.1 libstdc++6-4.6-dev_4.6.2-5+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.22-2+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.2-5+hurd.1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.1-1+hurd.1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-5+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-5+hurd.1 gcc-4.6-base_4.6.2-5+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20111106-1 hurd-dev_20111106-1 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libapt-pkg-dev_0.8.15.9 libattr1_1:2.4.46-5 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-8 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc0.3_2.13-24 libc0.3-dev_2.13-24 libc0.3-i686_2.13-24 libclass-isa-perl_0.36-2 libcomerr2_1.42-1 libcroco3_0.6.2-2 libcwidget3_0.5.16-3.1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.1 libept-dev_1.0.5 libept1_1.0.5 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libglib2.0-data_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.16-1 libgomp1_4.6.2-5+hurd.1 libgpg-error0_1.10-2 libldap-2.4-2_2.4.28-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.10-1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-4 libpopt0_1.16-3 libpthread-stubs0_0.3-3 libpthread-stubs0-dev_0.3-3 libquadmath0_4.6.2-5+hurd.1 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-2 libsasl2-modules_2.1.25.dfsg1-2 libsigc++-2.0-0c2a_2.2.9-1.1 libsigsegv2_2.9-4 libslang2_2.2.4-5 libsqlite3-0_3.7.9-3 libss2_1.42~WIP-2011-10-16-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-5+hurd.1 libstdc++6-4.6-dev_4.6.2-5+hurd.1 libswitch-perl_2.16-2 libtagcoll2-dev_2.0.13-1 libtasn1-3_2.11-1 libtext-iconv-perl_1.7-5 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libuuid1_2.19.1-5 libwibble-dev_0.1.26-1 libxapian-dev_1.2.7-1 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-5.1 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 pkg-config_0.26-1 po-debconf_1.0.16+nmu2 procps_1:3.2.8-11 psmisc_22.3-1 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 type-handling_0.2.23 tzdata_2011n-1 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 │
@@ -272,12 +283,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -287,30 +298,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -323,21 +329,21 @@ rm -f debian/stamp-patch*
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -355,7 +361,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -370,55 +376,60 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wfor
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.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]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+ * compiling Fasta.cpp
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -427,177 +438,173 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
* compiling genomeFile.cpp
- Building in src/annotateBed
- * compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+ * compiling annotateMain.cpp
* compiling annotateBed.cpp
- * linking annotateBed
- Building in src/bamToBed
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
* 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: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+ * compiling bedToBam.cpp
+
+- Building in src/bedpeToBam
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+ * compiling bedpeToBam.cpp
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterMain.cpp
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+ * compiling getOverlap.cpp
+
+- Building in src/groupBy
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
+ * compiling groupBy.cpp
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
- * compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling mergeMain.cpp
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
- * compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCovMain.cpp
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
+ * compiling pairToBedMain.cpp
+ * compiling pairToBed.cpp
- Building in src/pairToPair
- * compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling 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
+ * compiling pairToPairMain.cpp
+ * compiling pairToPair.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
- * compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling subtractMain.cpp
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
- * compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBamMain.cpp
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
- * compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
+ * compiling unionBedGraphsMain.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -636,62 +643,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../bedtools_2.14.3-1_hurd-i386.changes
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../bedtools_2.15.0-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_hurd-i386.deb'.
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-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-1158
+Build finished at 20120111-0824
-bedtools_2.14.3-1_hurd-i386.changes:
+bedtools_2.15.0-1_hurd-i386.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.14.3-1
+Version: 2.15.0-1
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-ironforge at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 78cec7a6dc1559b1477c22d1c3036be5c04d2b78 706072 bedtools_2.14.3-1_hurd-i386.deb
+ fa1d072696e136583ce07dafe49ebf0a8947e583 402344 bedtools_2.15.0-1_hurd-i386.deb
Checksums-Sha256:
- 5d896b34dce2b5c8bba0c6683c96c43fee283b0ef4530ebffd4e3991d10ee531 706072 bedtools_2.14.3-1_hurd-i386.deb
+ 5c9ab8161f838bb6ddd8b5386c60a04551aeadc70d3e9303010a7458e423dac3 402344 bedtools_2.15.0-1_hurd-i386.deb
Files:
- d53831595be0a04ce1b9d29268576cb0 706072 science optional bedtools_2.14.3-1_hurd-i386.deb
+ 240b0a7f1d5999b7ebd90b8328b5feac 402344 science optional bedtools_2.15.0-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_hurd-i386.deb
+bedtools_2.15.0-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 706072 bytes: control archive= 1767 bytes.
+ size 402344 bytes: control archive= 1868 bytes.
869 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4793
+ Installed-Size: 1279
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -707,50 +718,54 @@ bedtools_2.14.3-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 11:54 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 11:44 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/bin/
--rwxr-xr-x root/root 104532 2011-11-05 11:55 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223904 2011-11-05 11:55 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96364 2011-11-05 11:55 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 228132 2011-11-05 11:55 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121688 2011-11-05 11:55 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 122976 2011-11-05 11:55 ./usr/bin/closestBed
--rwxr-xr-x root/root 105832 2011-11-05 11:55 ./usr/bin/complementBed
--rwxr-xr-x root/root 285024 2011-11-05 11:55 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142684 2011-11-05 11:55 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114788 2011-11-05 11:55 ./usr/bin/flankBed
--rwxr-xr-x root/root 301428 2011-11-05 11:55 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350580 2011-11-05 11:55 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105984 2011-11-05 11:55 ./usr/bin/linksBed
--rwxr-xr-x root/root 109928 2011-11-05 11:55 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 108636 2011-11-05 11:55 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297452 2011-11-05 11:55 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 141472 2011-11-05 11:55 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 142848 2011-11-05 11:55 ./usr/bin/nucBed
--rwxr-xr-x root/root 88172 2011-11-05 11:55 ./usr/bin/overlap
--rwxr-xr-x root/root 366976 2011-11-05 11:55 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178292 2011-11-05 11:55 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129976 2011-11-05 11:55 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105704 2011-11-05 11:55 ./usr/bin/slopBed
--rwxr-xr-x root/root 143848 2011-11-05 11:55 ./usr/bin/sortBed
--rwxr-xr-x root/root 113436 2011-11-05 11:55 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272752 2011-11-05 11:55 ./usr/bin/tagBam
--rwxr-xr-x root/root 59976 2011-11-05 11:55 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285032 2011-11-05 11:55 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 11:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2012-01-05 02:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-01-02 11:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 07:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-11 08:23 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 08:20 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-01-02 11:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-01-02 11:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-01-02 11:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 11:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 08:24 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 36 2012-01-11 08:23 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-01-11 08:23 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-01-11 08:23 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1248424 2012-01-11 08:23 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-01-11 08:23 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-01-11 08:23 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-01-11 08:23 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 08:23 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-01-11 08:23 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 08:23 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-01-11 08:23 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-01-11 08:23 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-01-11 08:23 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 08:23 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-01-11 08:23 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-01-11 08:23 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-01-11 08:23 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-01-11 08:23 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-01-11 08:23 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-01-11 08:23 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-01-11 08:23 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-01-11 08:23 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-01-11 08:23 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-01-11 08:23 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-01-11 08:23 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-01-11 08:23 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -764,27 +779,28 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh
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:
+ libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
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:
+ libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
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, 0 newly installed, 17 to remove and 21 not upgraded.
-After this operation, 20.4 MB disk space will be freed.
-(Reading database ... 13440 files and directories currently installed.)
+ intltool-debian* libcroco3* libdb4.8* libexpat1* libmagic1* libsqlite3-0*
+ libunistring0* mime-support* po-debconf* python* python-minimal* python2.7*
+ python2.7-minimal* quilt*
+0 upgraded, 0 newly installed, 21 to remove and 28 not upgraded.
+After this operation, 32.2 MB disk space will be freed.
+(Reading database ... 15439 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -799,37 +815,43 @@ Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libdb4.8 ...
Removing libexpat1 ...
Purging configuration files for libexpat1 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 97260
-Build-Time: 846
+Build-Space: 62160
+Build-Time: 234
Distribution: sid
-Install-Time: 71
-Job: bedtools_2.14.3-1
+Install-Time: 42
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1125
-Source-Version: 2.14.3-1
-Space: 97260
+Package-Time: 358
+Source-Version: 2.15.0-1
+Space: 62160
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-1158
-Build needed 00:18:45, 97260k disc space
+Finished at 20120111-0824
+Build needed 00:05:58, 62160k disc space
diff --git a/i386.log b/i386.log
index fcba8c2..db2a33f 100644
--- a/i386.log
+++ b/i386.log
@@ -1,67 +1,68 @@
-From buildd at murphy.debian.org Sat Nov 05 02:00:38 2011
-Return-path: <buildd at murphy.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at biber.debian.org Wed Jan 11 07:19:45 2012
+Return-path: <buildd at biber.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
- id 1RMVYj-0008Cu-S1
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:37 +0000
-Received: from murphy.debian.org ([70.103.162.31])
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1RksTJ-0008EB-Dl
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:19:45 +0000
+Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
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)
- (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
- id 1RMVYi-0000ek-Qj
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:37 +0000
-Received: from buildd by murphy.debian.org with local (Exim 4.72)
- (envelope-from <buildd at murphy.debian.org>)
- id 1RMVYg-0005pu-SP; Sat, 05 Nov 2011 02:00:34 +0000
-Message-Id: <E1RMVYg-0005pu-SP at murphy.debian.org>
+ CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1RksTI-0000yy-Kr; Wed, 11 Jan 2012 07:19:44 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at biber.debian.org>)
+ id 1RksTH-0002Ax-Oa; Wed, 11 Jan 2012 07:19:43 +0000
+Message-Id: <E1RksTH-0002Ax-Oa at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 5 Nov 2011 02:00:34 +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_2.14.3-1 on i386 (dist=sid)
-Key-Id: B074D6C9
+Date: Wed, 11 Jan 2012 07:19:43 +0000
+From: buildd on biber <buildd at biber.debian.org>
+To: kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.15.0-1 on i386 (dist=sid)
+Key-Id: C83D412C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (i386) 05 Nov 2011 01:56 ║
+║ bedtools 2.15.0-1 (i386) 11 Jan 2012 07:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: i386
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://ftp.gr.debian.org unstable InRelease [189 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [6000 kB]
+Get:3 http://ftp.gr.debian.org unstable/contrib Sources [54.4 kB]
+Get:4 http://ftp.gr.debian.org unstable/non-free Sources [100 kB]
+Get:5 http://ftp.gr.debian.org unstable/main i386 Packages [7977 kB]
+Get:6 http://incoming.debian.org unstable InRelease [189 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.0 kB]
+Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2085 B]
+Ign http://ftp.gr.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Hit http://ftp.us.debian.org sid InRelease
-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/main Sources/DiffIndex
-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/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
-Get:3 http://incoming.debian.org Sources [25.7 kB]
-Get:4 http://incoming.debian.org Packages [300 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://ftp.us.debian.org sid/contrib Translation-en
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7977 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.0 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 328 kB in 4s (73.1 kB/s)
+Fetched 29.4 MB in 13s (2138 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +83,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 2s (330 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 2s (454 kB/s)
Download complete and in download only mode
Check arch
@@ -100,110 +101,171 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
-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 (5.9-2)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.09)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.1)
+mount: already installed (2.20.1-1.1)
+util-linux: already installed (2.20.1-1.1)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 19.1 MB of archives.
+After this operation, 52.4 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libncursesw5 i386 5.9-4 [330 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-5 [37.6 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main libssl1.0.0 i386 1.0.0e-3 [2862 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.30.2-4 [1822 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-5.1 [882 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-2 [122 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libexpat1 i386 2.0.1-7.2 [137 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libdb4.8 i386 4.8.30-11 [729 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.3 [203 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-3 [1014 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.09-2 [246 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.09-2 [51.5 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-5 [133 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main libsqlite3-0 i386 3.7.9-2 [436 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main python2.7-minimal i386 2.7.2-9 [1632 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main python2.7 i386 2.7.2-9 [2619 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.gr.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:26 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-5 [2025 kB]
+Get:27 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-2 [29.3 kB]
+Get:31 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 7 not upgraded.
-Need to get 0 B/9694 kB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
+Fetched 19.1 MB in 1s (15.6 MB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10722 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_i386.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10684 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_i386.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_i386.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_i386.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_i386.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_i386.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_i386.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_i386.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_i386.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_i386.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_i386.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_i386.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_i386.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_i386.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-9_i386.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously unselected package gettext.
@@ -211,49 +273,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
+Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libquadmath0_4.6.2-11 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,12 +338,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -280,24 +354,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -310,21 +384,21 @@ 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_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -357,41 +431,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -411,176 +494,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -619,62 +698,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.14.3-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.15.0-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0200
+Build finished at 20120111-0719
-bedtools_2.14.3-1_i386.changes:
+bedtools_2.15.0-1_i386.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
+Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 5cb5267c0ba90f19deb8065c4dc6383f8e15050a 703702 bedtools_2.14.3-1_i386.deb
+ c1cbde2217a5dd1ff2d8956e2b06429100909a16 402140 bedtools_2.15.0-1_i386.deb
Checksums-Sha256:
- 190d957c7b3fe6b270e9ecbc0baae04c370f18ec721f7876026f0c4faebe5d15 703702 bedtools_2.14.3-1_i386.deb
+ 917d0073e3a7147c70acc0a339329b28e3bedc5266160967374009e3cdcc99a2 402140 bedtools_2.15.0-1_i386.deb
Files:
- 7834daa25db8853a9098b1a19d9441bf 703702 science optional bedtools_2.14.3-1_i386.deb
+ 3853cf76f932189e25a03f756dcd5067 402140 science optional bedtools_2.15.0-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_i386.deb
+bedtools_2.15.0-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 703702 bytes: control archive= 1757 bytes.
+ size 402140 bytes: control archive= 1864 bytes.
864 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4782
+ Installed-Size: 1277
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -690,50 +773,54 @@ bedtools_2.14.3-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/bin/
--rwxr-xr-x root/root 121520 2011-11-05 02:00 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 141464 2011-11-05 02:00 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 301420 2011-11-05 02:00 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 272744 2011-11-05 02:00 ./usr/bin/tagBam
--rwxr-xr-x root/root 96356 2011-11-05 02:00 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 142360 2011-11-05 02:00 ./usr/bin/nucBed
--rwxr-xr-x root/root 143008 2011-11-05 02:00 ./usr/bin/sortBed
--rwxr-xr-x root/root 285024 2011-11-05 02:00 ./usr/bin/windowBed
--rwxr-xr-x root/root 122020 2011-11-05 02:00 ./usr/bin/closestBed
--rwxr-xr-x root/root 281864 2011-11-05 02:00 ./usr/bin/coverageBed
--rwxr-xr-x root/root 109600 2011-11-05 02:00 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 104524 2011-11-05 02:00 ./usr/bin/annotateBed
--rwxr-xr-x root/root 142420 2011-11-05 02:00 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 129456 2011-11-05 02:00 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 366968 2011-11-05 02:00 ./usr/bin/pairToBed
--rwxr-xr-x root/root 107064 2011-11-05 02:00 ./usr/bin/mergeBed
--rwxr-xr-x root/root 105472 2011-11-05 02:00 ./usr/bin/complementBed
--rwxr-xr-x root/root 297312 2011-11-05 02:00 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 88164 2011-11-05 02:00 ./usr/bin/overlap
--rwxr-xr-x root/root 178284 2011-11-05 02:00 ./usr/bin/pairToPair
--rwxr-xr-x root/root 105688 2011-11-05 02:00 ./usr/bin/linksBed
--rwxr-xr-x root/root 112756 2011-11-05 02:00 ./usr/bin/subtractBed
--rwxr-xr-x root/root 227744 2011-11-05 02:00 ./usr/bin/bedToBam
--rwxr-xr-x root/root 59648 2011-11-05 02:00 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 223548 2011-11-05 02:00 ./usr/bin/bamToBed
--rwxr-xr-x root/root 114204 2011-11-05 02:00 ./usr/bin/flankBed
--rwxr-xr-x root/root 350572 2011-11-05 02:00 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105344 2011-11-05 02:00 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 34 2012-01-11 07:19 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 36 2012-01-11 07:19 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 30 2012-01-11 07:19 ./usr/bin/flankBed
+-rwxr-xr-x root/root 29 2012-01-11 07:19 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 30 2012-01-11 07:19 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-01-11 07:19 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-01-11 07:19 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-01-11 07:19 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 1247172 2012-01-11 07:19 ./usr/bin/bedtools
+-rwxr-xr-x root/root 31 2012-01-11 07:19 ./usr/bin/windowBed
+-rwxr-xr-x root/root 34 2012-01-11 07:19 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 28 2012-01-11 07:19 ./usr/bin/tagBam
+-rwxr-xr-x root/root 32 2012-01-11 07:19 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 30 2012-01-11 07:19 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 32 2012-01-11 07:19 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-01-11 07:19 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-01-11 07:19 ./usr/bin/complementBed
+-rwxr-xr-x root/root 35 2012-01-11 07:19 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 36 2012-01-11 07:19 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 35 2012-01-11 07:19 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:19 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 34 2012-01-11 07:19 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 34 2012-01-11 07:19 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 32 2012-01-11 07:19 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-01-11 07:19 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 29 2012-01-11 07:19 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:16 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -747,73 +834,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-9ac3eda1-5379-41f1-b5fc-933636f6c548/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 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 7 not upgraded.
-After this operation, 27.3 MB disk space will be freed.
-(Reading database ... 12161 files and directories currently installed.)
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing cdbs ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing 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-i386-sbuild-67c75f87-be53-49e4-82b0-725c3ba5267a/build/buildd-bedtools_2.15.0-1-i386-1HqqaM
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 96784
-Build-Time: 212
+Build-Space: 62100
+Build-Time: 169
Distribution: sid
-Install-Time: 10
-Job: bedtools_2.14.3-1
+Install-Time: 58
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 236
-Source-Version: 2.14.3-1
-Space: 96784
+Package-Time: 258
+Source-Version: 2.15.0-1
+Space: 62100
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0200
-Build needed 00:03:56, 96784k disc space
-Signature with key 'B074D6C9' requested:
+Finished at 20120111-0719
+Build needed 00:04:18, 62100k disc space
+Signature with key 'C83D412C' requested:
diff --git a/ia64.log b/ia64.log
index eeeadfe..f230f75 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,67 +1,66 @@
-From buildd at alkman.debian.org Sat Nov 05 02:06:34 2011
-Return-path: <buildd at alkman.debian.org>
+From buildd at mundy.debian.org Wed Jan 11 07:22:42 2012
+Return-path: <buildd at mundy.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 alkman.debian.org>)
- id 1RMVeT-0000ZB-MY
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:06:33 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1RksW9-0000g5-S0
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:22:42 +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=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1RMVeR-0000vM-JX
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:06:32 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1RMVeP-0002kB-2X; Sat, 05 Nov 2011 02:06:29 +0000
-Date: Sat, 05 Nov 2011 02:06:29 +0000
-Message-Id: <E1RMVeP-0002kB-2X at alkman.debian.org>
-From: buildd on alkman <buildd at alkman.debian.org>
-To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on ia64 (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1RksW7-0003k1-CC; Wed, 11 Jan 2012 07:22:40 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1RksW4-0002L2-W8; Wed, 11 Jan 2012 07:22:37 +0000
+Date: Wed, 11 Jan 2012 07:22:36 +0000
+Message-Id: <E1RksW4-0002L2-W8 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_2.15.0-1 on ia64 (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 alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (ia64) 05 Nov 2011 01:54 ║
+║ bedtools 2.15.0-1 (ia64) 11 Jan 2012 07:11 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [5890 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [56.9 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [103 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [7529 kB]
+Get:1 http://spohr.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [6000 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [54.4 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [100 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [7645 kB]
Ign http://incoming.debian.org InRelease
Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5890 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.9 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.7 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2085 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7529 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.9 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7645 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.7 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 [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.9 MB in 23s (1187 kB/s)
+Fetched 28.7 MB in 18s (1565 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (887 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (856 kB/s)
Download complete and in download only mode
Check arch
@@ -109,7 +108,7 @@ Reading state information...
The following packages were automatically installed and are no longer required:
libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -117,36 +116,36 @@ Reading state information...
The following packages were automatically installed and are no longer required:
libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.3)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-3)
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)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -154,14 +153,15 @@ libc6.1-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
@@ -170,71 +170,109 @@ The following packages were automatically installed and are no longer required:
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
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 51 not upgraded.
-Need to get 11.4 MB of archives.
-After this operation, 38.5 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-4 [46.7 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 libglib2.0-0 ia64 2.28.8-1 [1992 kB]
-Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-5 [1177 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-2 [147 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.09-2 [271 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main file ia64 5.09-2 [54.4 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 62 not upgraded.
+Need to get 20.8 MB of archives.
+After this operation, 66.7 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ unstable/main libncursesw5 ia64 5.9-4 [387 kB]
+Get:2 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-5 [47.1 kB]
+Get:3 http://spohr.debian.org/debian/ unstable/main libssl1.0.0 ia64 1.0.0e-3 [1560 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main libffi5 ia64 3.0.10-3 [35.5 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.30.2-4 [2198 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-5.1 [1177 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-2 [147 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main libexpat1 ia64 2.0.1-7.2 [212 kB]
+Get:10 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libdb4.8 ia64 4.8.30-11 [1117 kB]
+Get:12 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
+Get:13 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-3 [1119 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.09-2 [271 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main file ia64 5.09-2 [54.4 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main libsqlite3-0 ia64 3.7.9-2 [631 kB]
+Get:19 http://spohr.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://spohr.debian.org/debian/ unstable/main python2.7-minimal ia64 2.7.2-9 [1988 kB]
+Get:21 http://spohr.debian.org/debian/ unstable/main python2.7 ia64 2.7.2-9 [2813 kB]
+Get:22 http://spohr.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://spohr.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
+Get:26 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 kB]
+Get:27 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.55-2 [37.2 kB]
+Get:31 http://spohr.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 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
-Fetched 11.4 MB in 1s (6326 kB/s)
+Fetched 20.8 MB in 19s (1042 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10648 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_ia64.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10538 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_ia64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_ia64.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_ia64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_ia64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_ia64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_ia64.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_ia64.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_ia64.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_ia64.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_ia64.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_ia64.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_ia64.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_ia64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_ia64.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_ia64.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_ia64.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-9_ia64.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously unselected package gettext.
@@ -242,39 +280,51 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_ia64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_ia64.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-9) ...
+Setting up python2.7 (2.7.2-9) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
@@ -283,11 +333,11 @@ Reading state information...
The following packages were automatically installed and are no longer required:
libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 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_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 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-5 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6.1-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libclass-isa-perl_0.36-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libppl-c4_0.11.2-6 libppl9_0.11.2-6 libpwl5_0.11.2-6 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsqlite3-0_3.7.9-2 libss2_1.42~WIP-2011-10-16-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 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-5.1 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -298,12 +348,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -313,30 +363,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS =
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -349,21 +394,21 @@ 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_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -381,7 +426,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -396,41 +441,54 @@ g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)':
+src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
+src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -d lib ] || mkdir -p lib
[ -d include ] || mkdir -p include
[ -d include/api ] || mkdir -p include/api
[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
-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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -441,10 +499,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -454,176 +508,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -662,65 +712,68 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
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/multiBamCov 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/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/tagBam debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed debian/bedtools/usr/bin/multiIntersectBed" were not uselessly linked against it (they use none of its symbols).
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.14.3-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.15.0-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0206
+Build finished at 20120111-0722
-bedtools_2.14.3-1_ia64.changes:
+bedtools_2.15.0-1_ia64.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman 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
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 74974e8197a045607b945be9187fc45d42cb4eff 771472 bedtools_2.14.3-1_ia64.deb
+ 13ffad7622df6d784dfd1f7114be353c6439f8db 500864 bedtools_2.15.0-1_ia64.deb
Checksums-Sha256:
- 8e3bb00d4352a3083bb8f8ae61dcf8efae773d26e8f0c25f5c2d3fa684cdba46 771472 bedtools_2.14.3-1_ia64.deb
+ 0010e3bac861b4c0bf31986e6f9887ddd4085670522a0d6aa066174578434a66 500864 bedtools_2.15.0-1_ia64.deb
Files:
- 05d1f311850f304e6d8c650ec3896f5e 771472 science optional bedtools_2.14.3-1_ia64.deb
+ 4968cb15350537dc0c7cbbcad2f51458 500864 science optional bedtools_2.15.0-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_ia64.deb
+bedtools_2.15.0-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 771472 bytes: control archive= 1775 bytes.
- 880 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ size 500864 bytes: control archive= 1875 bytes.
+ 878 bytes, 19 lines control
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9814
+ Installed-Size: 2616
Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6.1 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
+ 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
@@ -734,50 +787,54 @@ bedtools_2.14.3-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/bin/
--rwxr-xr-x root/root 216784 2011-11-05 02:05 ./usr/bin/annotateBed
--rwxr-xr-x root/root 463184 2011-11-05 02:05 ./usr/bin/bamToBed
--rwxr-xr-x root/root 199664 2011-11-05 02:05 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 472096 2011-11-05 02:05 ./usr/bin/bedToBam
--rwxr-xr-x root/root 246984 2011-11-05 02:05 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 251936 2011-11-05 02:05 ./usr/bin/closestBed
--rwxr-xr-x root/root 220104 2011-11-05 02:05 ./usr/bin/complementBed
--rwxr-xr-x root/root 580520 2011-11-05 02:05 ./usr/bin/coverageBed
--rwxr-xr-x root/root 293872 2011-11-05 02:05 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 234680 2011-11-05 02:05 ./usr/bin/flankBed
--rwxr-xr-x root/root 612264 2011-11-05 02:05 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 728464 2011-11-05 02:05 ./usr/bin/intersectBed
--rwxr-xr-x root/root 220504 2011-11-05 02:05 ./usr/bin/linksBed
--rwxr-xr-x root/root 226504 2011-11-05 02:05 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 221304 2011-11-05 02:05 ./usr/bin/mergeBed
--rwxr-xr-x root/root 620864 2011-11-05 02:05 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 290176 2011-11-05 02:05 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 297608 2011-11-05 02:05 ./usr/bin/nucBed
--rwxr-xr-x root/root 178912 2011-11-05 02:05 ./usr/bin/overlap
--rwxr-xr-x root/root 767872 2011-11-05 02:05 ./usr/bin/pairToBed
--rwxr-xr-x root/root 378256 2011-11-05 02:05 ./usr/bin/pairToPair
--rwxr-xr-x root/root 270936 2011-11-05 02:05 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 217448 2011-11-05 02:05 ./usr/bin/slopBed
--rwxr-xr-x root/root 306000 2011-11-05 02:05 ./usr/bin/sortBed
--rwxr-xr-x root/root 235192 2011-11-05 02:05 ./usr/bin/subtractBed
--rwxr-xr-x root/root 565216 2011-11-05 02:05 ./usr/bin/tagBam
--rwxr-xr-x root/root 120416 2011-11-05 02:05 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 587992 2011-11-05 02:05 ./usr/bin/windowBed
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:13 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-11 07:22 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 32 2012-01-11 07:22 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 35 2012-01-11 07:22 ./usr/bin/complementBed
+-rwxr-xr-x root/root 31 2012-01-11 07:22 ./usr/bin/windowBed
+-rwxr-xr-x root/root 2617920 2012-01-11 07:22 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-01-11 07:22 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-01-11 07:22 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 29 2012-01-11 07:22 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-01-11 07:22 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-01-11 07:22 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 36 2012-01-11 07:22 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 28 2012-01-11 07:22 ./usr/bin/nucBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:22 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-01-11 07:22 ./usr/bin/closestBed
+-rwxr-xr-x root/root 34 2012-01-11 07:22 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 36 2012-01-11 07:22 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 28 2012-01-11 07:22 ./usr/bin/tagBam
+-rwxr-xr-x root/root 28 2012-01-11 07:22 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 30 2012-01-11 07:22 ./usr/bin/linksBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 35 2012-01-11 07:22 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 34 2012-01-11 07:22 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 35 2012-01-11 07:22 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:22 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 34 2012-01-11 07:22 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 34 2012-01-11 07:22 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 30 2012-01-11 07:22 ./usr/bin/flankBed
+-rwxr-xr-x root/root 32 2012-01-11 07:22 ./usr/bin/clusterBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -791,7 +848,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-0c108c67-886e-4139-903f-811a245b5655/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-3830c53a-73f0-493d-af9d-3152f21444bb/build/buildd-bedtools_2.15.0-1-ia64-bPioEU
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -799,19 +856,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 166952
-Build-Time: 602
+Build-Space: 111456
+Build-Time: 516
Distribution: sid
-Install-Time: 65
-Job: bedtools_2.14.3-1
+Install-Time: 113
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 725
-Source-Version: 2.14.3-1
-Space: 166952
+Package-Time: 683
+Source-Version: 2.15.0-1
+Space: 111456
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0206
-Build needed 00:12:05, 166952k disc space
-Signature with key 'FC1E8668' requested:
+Finished at 20120111-0722
+Build needed 00:11:23, 111456k disc space
+Signature with key '66C872EA' requested:
diff --git a/info b/info
index 042d53c..a3475de 100644
--- a/info
+++ b/info
@@ -1,13 +1,13 @@
-s390~1320458404~sid~successful
-powerpc~1320458428~sid~successful
-i386~1320458438~sid~successful
-ia64~1320458794~sid~successful
-mipsel~1320459306~sid~successful
-armel~1320459658~sid~successful
-sparc~1320460114~sid~successful
-mips~1320460447~sid~successful
-kfreebsd-i386~1320463028~sid~successful
-kfreebsd-amd64~1320463952~sid~successful
-hurd-i386~1320494343~sid~successful
-s390x~1322367602~sid~successful
-armhf~1322509076~sid~successful
+s390~1326265966~sid~successful
+powerpc~1326266131~sid~successful
+s390x~1326266144~sid~successful
+i386~1326266386~sid~successful
+kfreebsd-i386~1326266425~sid~successful
+ia64~1326266562~sid~successful
+hurd-i386~1326266673~sid~successful
+kfreebsd-amd64~1326266868~sid~successful
+armhf~1326267222~sid~successful
+sparc~1326267270~sid~successful
+mips~1326267970~sid~successful
+armel~1326272090~sid~successful
+mipsel~1326277894~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index f086694..5661425 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,30 +1,30 @@
-From buildd at fano.debian.org Sat Nov 05 03:32:31 2011
+From buildd at fano.debian.org Wed Jan 11 07:27:40 2012
Return-path: <buildd at fano.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 fano.debian.org>)
- id 1RMWzf-0006Nk-Gj
- for logs at buildd.debian.org; Sat, 05 Nov 2011 03:32:31 +0000
+ id 1Rksax-0001WJ-Qz
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:27:39 +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 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 fano.debian.org>)
- id 1RMWze-00046C-A6; Sat, 05 Nov 2011 03:32:30 +0000
+ id 1Rksaw-0001Mk-Nj; Wed, 11 Jan 2012 07:27:39 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1RMWzb-000Iui-Qp; Sat, 05 Nov 2011 03:32:27 +0000
-Message-Id: <E1RMWzb-000Iui-Qp at fano.debian.org>
+ id 1Rksau-0000ZP-Cu; Wed, 11 Jan 2012 07:27:36 +0000
+Message-Id: <E1Rksau-0000ZP-Cu 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: Sat, 5 Nov 2011 03:32:27 +0000
+Date: Wed, 11 Jan 2012 07:27:36 +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_2.14.3-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.15.0-1 on kfreebsd-amd64
(dist=sid)
Key-Id: D33FE1D8
Delivered-To: logs at buildd.debian.org
@@ -32,62 +32,46 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (kfreebsd-amd64) 05 Nov 2011 03:26 ║
+║ bedtools 2.15.0-1 (kfreebsd-amd64) 11 Jan 2012 07:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:4 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:5 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
-Get:6 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:7 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid InRelease
+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
-Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:9 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:10 http://incoming.debian.org Release [1604 B]
-Get:11 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:12 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:13 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:14 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
-Get:15 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [87.5 kB]
-Get:16 http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex [2023 B]
-Get:17 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:18 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
+Get:2 http://incoming.debian.org Release [1616 B]
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+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
Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:19 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:20 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:21 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:22 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:23 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:24 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:25 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
-Get:26 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [87.5 kB]
-Get:27 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:28 http://incoming.debian.org Sources [26.0 kB]
-Get:29 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
+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
-Get:30 http://incoming.debian.org Packages [299 kB]
-Get:31 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:3 http://incoming.debian.org Sources [49.9 kB]
+Get:4 http://incoming.debian.org Packages [601 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
-Get:32 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:33 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:34 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
-Fetched 902 kB in 26s (34.3 kB/s)
+Fetched 654 kB in 3s (167 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -108,11 +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 928 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (16.3 MB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (664 kB/s)
Download complete and in download only mode
Check arch
@@ -126,103 +110,126 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1)
-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 (5.9-2)
+freebsd-utils: already installed (8.2+ds3-2)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.09)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.25-3)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-4)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
+ libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
- procmail graphviz
+ python-doc python-tk python2.7-doc binfmt-support procmail graphviz
+ default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
- po-debconf quilt zlib1g-dev
+ libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python
+ python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 8 not upgraded.
-Need to get 0 B/8237 kB of archives.
-After this operation, 21.6 MB of additional disk space will be used.
+0 upgraded, 27 newly installed, 0 to remove and 11 not upgraded.
+Need to get 0 B/15.4 MB of archives.
+After this operation, 41.9 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 12289 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-amd64.deb) ...
+(Reading database ... 11850 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_kfreebsd-amd64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_kfreebsd-amd64.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.09-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_kfreebsd-amd64.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_kfreebsd-amd64.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_kfreebsd-amd64.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext.
@@ -230,44 +237,54 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
-Setting up man-db (2.6.0.2-2) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 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_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 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_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 kfreebsd-kernel-headers_0.62 libc0.1-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds3-2 g++_4:4.6.2-3 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-14 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds3-2 kfreebsd-kernel-headers_0.62 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc0.1_2.13-24 libc0.1-dev_2.13-24 libcam0_8.2+ds2-1 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds2-1 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.16-1 libgomp1_4.6.2-11 libgpg-error0_1.10-2 libgssglue1_0.3-4 libjail1_8.2+ds2-1 libkiconv4_8.2+ds2-1 libkvm0_8.2+ds2-1 libldap-2.4-2_2.4.25-4+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.10-1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-4 libquadmath0_4.6.2-11 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds2-1 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtasn1-3_2.11-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5.1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.2.8-11 psmisc_22.13-1 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 type-handling_0.2.23 tzdata_2011n-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -278,12 +295,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -294,24 +311,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -324,21 +341,21 @@ 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_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -371,41 +388,54 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)':
+src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
+src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -d lib ] || mkdir -p lib
[ -d include ] || mkdir -p include
[ -d include/api ] || mkdir -p include/api
[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
-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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -425,176 +455,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -633,28 +659,29 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.14.3-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.15.0-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0332
+Build finished at 20120111-0724
-bedtools_2.14.3-1_kfreebsd-amd64.changes:
+bedtools_2.15.0-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -662,33 +689,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 672ddf8e5d47d16fc7ed858b108e604374d14334 692318 bedtools_2.14.3-1_kfreebsd-amd64.deb
+ aec4a53f8605e224da0099dfc63c5760f0948511 394590 bedtools_2.15.0-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 9342060799ef754f67dc2f26d3193b8e8c1f9d7cc80a7d128118d5f7fdd1799c 692318 bedtools_2.14.3-1_kfreebsd-amd64.deb
+ 1aac10e7ccacbc8ac69d38ef06af1f6d8aed39f3ed3ed1eb720ca31bdc11dc46 394590 bedtools_2.15.0-1_kfreebsd-amd64.deb
Files:
- 651259a21f1a21ef63ee37d59de363c5 692318 science optional bedtools_2.14.3-1_kfreebsd-amd64.deb
+ 56b50754fd92e7ecaa50d84ad86e3dce 394590 science optional bedtools_2.15.0-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_kfreebsd-amd64.deb
+bedtools_2.15.0-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 692318 bytes: control archive= 1762 bytes.
+ size 394590 bytes: control archive= 1874 bytes.
876 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4809
+ Installed-Size: 1241
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -704,50 +734,54 @@ bedtools_2.14.3-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 03:28 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/bin/
--rwxr-xr-x root/root 110000 2011-11-05 03:31 ./usr/bin/annotateBed
--rwxr-xr-x root/root 218376 2011-11-05 03:31 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101856 2011-11-05 03:31 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 229232 2011-11-05 03:31 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126480 2011-11-05 03:31 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126656 2011-11-05 03:31 ./usr/bin/closestBed
--rwxr-xr-x root/root 114168 2011-11-05 03:31 ./usr/bin/complementBed
--rwxr-xr-x root/root 276624 2011-11-05 03:31 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147112 2011-11-05 03:31 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 118920 2011-11-05 03:31 ./usr/bin/flankBed
--rwxr-xr-x root/root 294888 2011-11-05 03:31 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 345672 2011-11-05 03:31 ./usr/bin/intersectBed
--rwxr-xr-x root/root 110248 2011-11-05 03:31 ./usr/bin/linksBed
--rwxr-xr-x root/root 118328 2011-11-05 03:31 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114112 2011-11-05 03:31 ./usr/bin/mergeBed
--rwxr-xr-x root/root 292912 2011-11-05 03:31 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 147016 2011-11-05 03:31 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 147136 2011-11-05 03:31 ./usr/bin/nucBed
--rwxr-xr-x root/root 93664 2011-11-05 03:31 ./usr/bin/overlap
--rwxr-xr-x root/root 356352 2011-11-05 03:31 ./usr/bin/pairToBed
--rwxr-xr-x root/root 180096 2011-11-05 03:31 ./usr/bin/pairToPair
--rwxr-xr-x root/root 135416 2011-11-05 03:31 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110232 2011-11-05 03:31 ./usr/bin/slopBed
--rwxr-xr-x root/root 150952 2011-11-05 03:31 ./usr/bin/sortBed
--rwxr-xr-x root/root 118192 2011-11-05 03:31 ./usr/bin/subtractBed
--rwxr-xr-x root/root 267792 2011-11-05 03:31 ./usr/bin/tagBam
--rwxr-xr-x root/root 65032 2011-11-05 03:31 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 278952 2011-11-05 03:31 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2012-01-11 07:23 ./
+drwxr-xr-x root/root 0 2012-01-11 07:23 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:24 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:24 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-11 07:24 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:18 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 07:24 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 36 2012-01-11 07:23 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-01-11 07:23 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-01-11 07:23 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1242088 2012-01-11 07:24 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-01-11 07:23 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-01-11 07:23 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-01-11 07:23 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:23 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-01-11 07:23 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 07:23 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-01-11 07:23 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-01-11 07:23 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-01-11 07:23 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:23 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-01-11 07:23 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-01-11 07:23 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-01-11 07:23 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-01-11 07:23 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-01-11 07:23 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-01-11 07:23 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-01-11 07:23 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-01-11 07:23 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-01-11 07:23 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-01-11 07:23 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-01-11 07:23 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-01-11 07:23 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -761,21 +795,23 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1320463619-70245/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1326266062-99271/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
- libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 8 not upgraded.
-After this operation, 21.6 MB disk space will be freed.
-(Reading database ... 13465 files and directories currently installed.)
+ intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0* libmagic1*
+ libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db*
+ mime-support* po-debconf* python* python-minimal* python2.7*
+ python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 27 to remove and 11 not upgraded.
+After this operation, 41.9 MB disk space will be freed.
+(Reading database ... 13938 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -790,18 +826,34 @@ Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libdb4.8 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
+Removing libffi5 ...
+Purging configuration files for libffi5 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
Removing man-db ...
Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
+Removing libssl1.0.0 ...
+Purging configuration files for libssl1.0.0 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -809,18 +861,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 139476
-Build-Time: 225
+Build-Space: 101320
+Build-Time: 351
Distribution: sid
-Install-Time: 41
-Job: bedtools_2.14.3-1
+Install-Time: 217
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 304
-Source-Version: 2.14.3-1
-Space: 139476
+Package-Time: 593
+Source-Version: 2.15.0-1
+Space: 101320
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0332
-Build needed 00:05:04, 139476k disc space
+Finished at 20120111-0724
+Build needed 00:09:53, 101320k disc space
Signature with key 'D33FE1D8' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 76c1772..ae37178 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,91 +1,73 @@
-From buildd at finzi.debian.org Sat Nov 05 03:17:08 2011
-Return-path: <buildd at finzi.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at field.debian.org Wed Jan 11 07:20:24 2012
+Return-path: <buildd at field.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RMWkm-0003Rm-77
- for logs at buildd.debian.org; Sat, 05 Nov 2011 03:17:08 +0000
-Received: from finzi.debian.org ([206.12.19.111])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RMWkk-0003XY-EX; Sat, 05 Nov 2011 03:17:07 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1RMWkh-000GWL-Rp; Sat, 05 Nov 2011 03:17:03 +0000
-Message-Id: <E1RMWkh-000GWL-Rp at finzi.debian.org>
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1RksTw-0008Pw-JX
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:20:24 +0000
+Received: from field.debian.org ([194.177.211.210])
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1RksTv-0000zf-J2; Wed, 11 Jan 2012 07:20:23 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1RksTu-000CxQ-4V; Wed, 11 Jan 2012 07:20:22 +0000
+Message-Id: <E1RksTu-000CxQ-4V 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: Sat, 5 Nov 2011 03:17:03 +0000
-From: buildd on finzi <buildd at finzi.debian.org>
+Date: Wed, 11 Jan 2012 07:20:22 +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_2.14.3-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.15.0-1 on kfreebsd-i386
(dist=sid)
-Key-Id: D859A500
+Key-Id: 65BA331C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (kfreebsd-i386) 05 Nov 2011 03:12 ║
+║ bedtools 2.15.0-1 (kfreebsd-i386) 11 Jan 2012 07:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: kfreebsd-i386
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:4 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:5 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
-Get:6 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:7 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+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
+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
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:9 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:10 http://incoming.debian.org Release [1604 B]
-Get:11 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:12 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:13 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:14 http://incoming.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
-Get:15 http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex [2023 B]
-Get:16 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:17 http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:18 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:19 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:20 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:21 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
-Get:22 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:23 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:24 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
-Get:25 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:26 http://incoming.debian.org Sources [26.4 kB]
-Get:27 http://incoming.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Get:28 http://incoming.debian.org Packages [299 kB]
+Get:2 http://incoming.debian.org Release [1616 B]
+Get:3 http://incoming.debian.org Sources [49.9 kB]
+Get:4 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
-Get:29 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
Ign http://incoming.debian.org Translation-en
-Get:30 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
-Get:31 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
-Get:32 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
-Fetched 722 kB in 17s (41.6 kB/s)
+Fetched 654 kB in 6s (97.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -106,11 +88,11 @@ 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 928 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (17.2 MB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 3s (294 kB/s)
Download complete and in download only mode
Check arch
@@ -124,103 +106,129 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1)
-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 (5.9-2)
+freebsd-utils: already installed (8.2+ds3-2)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.09)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.25-3)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-4)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
+ python-minimal python2.7 python2.7-minimal
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
- procmail graphviz
+ python-doc python-tk python2.7-doc binfmt-support procmail graphviz
+ default-mta mail-transport-agent
Recommended packages:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
- po-debconf quilt zlib1g-dev
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1
+ libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
+ mime-support po-debconf python python-minimal python2.7 python2.7-minimal
+ quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 17 not upgraded.
-Need to get 0 B/8099 kB of archives.
-After this operation, 21.1 MB of additional disk space will be used.
+0 upgraded, 28 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/16.3 MB of archives.
+After this operation, 44.1 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 14030 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-i386.deb) ...
+(Reading database ... 11527 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_kfreebsd-i386.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_kfreebsd-i386.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_kfreebsd-i386.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.09-2_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_kfreebsd-i386.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_kfreebsd-i386.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_kfreebsd-i386.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext.
@@ -228,44 +236,55 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
-Setting up man-db (2.6.0.2-2) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
-Package versions: apt_0.8.15.9 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 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_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.12-1 libgomp1_4.6.2-3 libgpg-error0_1.10-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 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_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 tzdata_2011n-1 util-linux_2.19.1-5 vim_2:7.3.346-1 vim-common_2:7.3.346-1 vim-runtime_2:7.3.346-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 kfreebsd-kernel-headers_0.62 libc0.1-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds3-2 g++_4:4.6.2-3 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-10 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds3-2 kfreebsd-kernel-headers_0.62 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc0.1_2.13-24 libc0.1-dev_2.13-24 libcam0_8.2+ds1-4 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 libgssglue1_0.3-4 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds2-2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-4 libquadmath0_4.6.2-11 libreadline6_6.2-8 libsbuf0_8.2+ds1-4 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5.1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.2.8-11 psmisc_22.13-1 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 type-handling_0.2.23 tzdata_2011n-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -276,12 +295,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -292,24 +311,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -322,21 +341,21 @@ 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_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -369,41 +388,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -423,176 +451,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -631,62 +655,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.14.3-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.15.0-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0316
+Build finished at 20120111-0719
-bedtools_2.14.3-1_kfreebsd-i386.changes:
+bedtools_2.15.0-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
+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
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- f3abe30f037aa655a0ae4e5d795109fabc65a549 702966 bedtools_2.14.3-1_kfreebsd-i386.deb
+ 4c61e91d0123b00aa458bf4efdd149949e774ce0 402204 bedtools_2.15.0-1_kfreebsd-i386.deb
Checksums-Sha256:
- 486c7bf303b6a707117ff061ba344cacf3d2472238184ddb4fb10cd3ecf85ccd 702966 bedtools_2.14.3-1_kfreebsd-i386.deb
+ 2abf1b1251c2005b38adf49c7110ddd84dde20f975e7ebeab8dc5d808655c246 402204 bedtools_2.15.0-1_kfreebsd-i386.deb
Files:
- 5268f6a056f030ce7f202baccc482e30 702966 science optional bedtools_2.14.3-1_kfreebsd-i386.deb
+ 3ba4aae440c04a84ffc031f1a9eaccce 402204 science optional bedtools_2.15.0-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_kfreebsd-i386.deb
+bedtools_2.15.0-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 702966 bytes: control archive= 1769 bytes.
+ size 402204 bytes: control archive= 1872 bytes.
875 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4749
+ Installed-Size: 1247
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -702,50 +730,54 @@ bedtools_2.14.3-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 03:13 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/bin/
--rwxr-xr-x root/root 103224 2011-11-05 03:16 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223468 2011-11-05 03:16 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96356 2011-11-05 03:16 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227672 2011-11-05 03:16 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121488 2011-11-05 03:16 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 121988 2011-11-05 03:16 ./usr/bin/closestBed
--rwxr-xr-x root/root 105440 2011-11-05 03:16 ./usr/bin/complementBed
--rwxr-xr-x root/root 281784 2011-11-05 03:16 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142452 2011-11-05 03:16 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114172 2011-11-05 03:16 ./usr/bin/flankBed
--rwxr-xr-x root/root 301420 2011-11-05 03:16 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350572 2011-11-05 03:16 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105656 2011-11-05 03:16 ./usr/bin/linksBed
--rwxr-xr-x root/root 109568 2011-11-05 03:16 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 107032 2011-11-05 03:16 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297312 2011-11-05 03:16 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 141464 2011-11-05 03:16 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 142392 2011-11-05 03:16 ./usr/bin/nucBed
--rwxr-xr-x root/root 88164 2011-11-05 03:16 ./usr/bin/overlap
--rwxr-xr-x root/root 366968 2011-11-05 03:16 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178284 2011-11-05 03:16 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129424 2011-11-05 03:16 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105312 2011-11-05 03:16 ./usr/bin/slopBed
--rwxr-xr-x root/root 142976 2011-11-05 03:16 ./usr/bin/sortBed
--rwxr-xr-x root/root 112716 2011-11-05 03:16 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272744 2011-11-05 03:16 ./usr/bin/tagBam
--rwxr-xr-x root/root 59616 2011-11-05 03:16 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285024 2011-11-05 03:16 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2012-01-11 07:18 ./
+drwxr-xr-x root/root 0 2012-01-11 07:18 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:16 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 07:19 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 36 2012-01-11 07:18 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-01-11 07:18 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-01-11 07:18 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1247548 2012-01-11 07:19 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-01-11 07:18 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-01-11 07:18 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-01-11 07:18 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:18 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-01-11 07:18 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 07:18 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-01-11 07:18 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-01-11 07:18 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-01-11 07:18 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:18 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-01-11 07:18 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-01-11 07:18 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-01-11 07:18 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-01-11 07:18 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-01-11 07:18 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-01-11 07:18 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-01-11 07:18 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-01-11 07:18 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-01-11 07:18 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-01-11 07:18 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-01-11 07:18 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-01-11 07:18 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -759,21 +791,23 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1320462740-60635/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1326266009-46743/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
- libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 17 not upgraded.
-After this operation, 21.1 MB disk space will be freed.
-(Reading database ... 15204 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0*
+ libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2*
+ man-db* mime-support* po-debconf* python* python-minimal* python2.7*
+ python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 28 to remove and 10 not upgraded.
+After this operation, 44.1 MB disk space will be freed.
+(Reading database ... 13797 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -784,22 +818,40 @@ Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libdb4.8 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
+Removing libffi5 ...
+Purging configuration files for libffi5 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing man-db ...
-Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
+Removing libssl1.0.0 ...
+Purging configuration files for libssl1.0.0 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -807,18 +859,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 97874
-Build-Time: 196
+Build-Space: 62552
+Build-Time: 186
Distribution: sid
-Install-Time: 36
-Job: bedtools_2.14.3-1
+Install-Time: 124
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 261
-Source-Version: 2.14.3-1
-Space: 97874
+Package-Time: 337
+Source-Version: 2.15.0-1
+Space: 62552
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0316
-Build needed 00:04:21, 97874k disc space
-Signature with key 'D859A500' requested:
+Finished at 20120111-0719
+Build needed 00:05:37, 62552k disc space
+Signature with key '65BA331C' requested:
diff --git a/mips.log b/mips.log
index 16978a0..651abc3 100644
--- a/mips.log
+++ b/mips.log
@@ -1,68 +1,68 @@
-From buildd at lucatelli.debian.org Sat Nov 05 02:34:06 2011
-Return-path: <buildd at lucatelli.debian.org>
+From buildd2 at lucatelli.debian.org Wed Jan 11 07:45:58 2012
+Return-path: <buildd2 at lucatelli.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 1RMW4N-0004Hw-EW
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:51 +0000
+ (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
+ id 1Rkssf-0004ld-VX
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:45:58 +0000
Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
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)
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 1RMW49-0005I0-5z
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:05 +0000
-Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lucatelli.debian.org>) id 1RMW47-0007z5-D1
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:03 +0000
-From: buildd on lucatelli <buildd at lucatelli.debian.org>
+ (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
+ id 1Rksse-0002EG-7Y
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:45:56 +0000
+Received: from buildd2 by lucatelli.debian.org with local (Exim 4.69)
+ (envelope-from <buildd2 at lucatelli.debian.org>) id 1Rkssg-0001rZ-SA
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:45:58 +0000
+From: buildd on lucatelli <buildd2 at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on mips (dist=sid)
+Subject: Log for successful build of bedtools_2.15.0-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RMW47-0007z5-D1 at lucatelli.debian.org>
-Date: Sat, 05 Nov 2011 02:33:03 +0000
+Message-Id: <E1Rkssg-0001rZ-SA at lucatelli.debian.org>
+Date: Wed, 11 Jan 2012 07:45:58 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (mips) 05 Nov 2011 01:54 ║
+║ bedtools 2.15.0-1 (mips) 11 Jan 2012 07:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: mips
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5890 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6000 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 [5890 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [56.9 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7603 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.8 kB]
+Get:5 http://incoming.debian.org Release [1616 B]
+Get:6 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [54.4 kB]
+Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [100 kB]
+Get:9 http://mirror-ubc.debian.org unstable/main mips Packages [7732 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.7 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2085 B]
Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7603 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.8 kB]
+Get:12 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:14 http://incoming.debian.org unstable/main mips Packages [7732 kB]
+Get:15 http://incoming.debian.org unstable/contrib mips Packages [55.7 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 [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.0 MB in 1min 16s (366 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 28.9 MB in 1min 24s (344 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (703 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (838 kB/s)
Download complete and in download only mode
Check arch
@@ -107,19 +107,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 58 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -127,21 +127,21 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-3)
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)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -149,84 +149,123 @@ libc6-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 38 not upgraded.
-Need to get 9581 kB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-4 [35.3 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.8-1 [1565 kB]
-Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 58 not upgraded.
+Need to get 17.1 MB of archives.
+After this operation, 49.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 mips 5.9-4 [307 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-5 [35.4 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libssl1.0.0 mips 1.0.0e-3 [1085 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.30.2-4 [1751 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5.1 [858 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libexpat1 mips 2.0.1-7.2 [143 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libdb4.8 mips 4.8.30-11 [661 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-3 [984 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 mips 3.7.9-2 [448 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main python2.7-minimal mips 2.7.2-8 [1698 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main python2.7 mips 2.7.2-8 [2572 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-2 [28.6 kB]
+Get:31 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://mirror-ubc.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 9581 kB in 1s (6304 kB/s)
+Fetched 17.1 MB in 2s (5808 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10643 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_mips.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10544 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mips.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_mips.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_mips.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_mips.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mips.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mips.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_mips.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mips.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mips.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mips.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mips.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_mips.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_mips.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_mips.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mips.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_mips.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-8_mips.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-8_mips.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously unselected package gettext.
@@ -234,49 +273,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_mips.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_mips.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-8) ...
+Setting up python2.7 (2.7.2-8) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-6
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsqlite3-0_3.7.9-2 libss2_1.42~WIP-2011-10-16-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.0.0-6 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-8 python2.7-minimal_2.7.2-8 quilt_0.50-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -286,13 +337,13 @@ Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,30 +353,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -338,21 +384,21 @@ 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_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -370,7 +416,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -385,41 +431,50 @@ g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -430,10 +485,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -443,176 +494,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -651,64 +698,68 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../bedtools_2.14.3-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../bedtools_2.15.0-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0232
+Build finished at 20120111-0745
-bedtools_2.14.3-1_mips.changes:
+bedtools_2.15.0-1_mips.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 470d53e53208c78df490b9b29e1b12f51efcfdcc 617236 bedtools_2.14.3-1_mips.deb
+ 18ab6a1e16b7c6b81e9e55f9796f521e20b4e375 324664 bedtools_2.15.0-1_mips.deb
Checksums-Sha256:
- af2e136e7d389e5695cb3ccc6f7b282c288381cb40c24995cb7fd5d385e36e25 617236 bedtools_2.14.3-1_mips.deb
+ 1c3d6f313dc1f80c392a649bc5e7da8be91efd3d7344cb8313c25c623dbd85d8 324664 bedtools_2.15.0-1_mips.deb
Files:
- 622dd08fe7e3645aff5a03d0a16feef9 617236 science optional bedtools_2.14.3-1_mips.deb
+ a1f13a5324b04f5c71b0cf3e060d8ae0 324664 science optional bedtools_2.15.0-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_mips.deb
+bedtools_2.15.0-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 617236 bytes: control archive= 1756 bytes.
- 866 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ size 324664 bytes: control archive= 1872 bytes.
+ 864 bytes, 19 lines control
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5161
+ Installed-Size: 1345
Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ 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
@@ -722,7 +773,7 @@ bedtools_2.14.3-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-919d1dd9-220f-451b-9cdd-e921ba7947de/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools_2.14.3-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-56da54ba-13fe-4f72-8e32-a6c8efd538e7/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools_2.15.0-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -736,31 +787,33 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-919d1dd9-220f-451b-9cdd-e921ba7947de/build/buildd-bedtools_2.14.3-1-mips-INFNuP
+Purging /var/lib/schroot/mount/sid-mips-sbuild-56da54ba-13fe-4f72-8e32-a6c8efd538e7/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo
Not cleaning session: cloned chroot in use
+Can't open average time db /var/lib/sbuild/avg-build-times
+Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 105080
-Build-Time: 2105
+Build-Space: 67684
+Build-Time: 1976
Distribution: sid
-Install-Time: 72
-Job: bedtools_2.14.3-1
+Install-Time: 126
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 2299
-Source-Version: 2.14.3-1
-Space: 105080
+Package-Time: 2233
+Source-Version: 2.15.0-1
+Space: 67684
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0232
-Build needed 00:38:19, 105080k disc space
+Finished at 20120111-0745
+Build needed 00:37:13, 67684k disc space
Signature with key '7A0A8DA2' requested:
-From buildd at mayer.debian.org Sat Nov 05 02:15:06 2011
+From buildd at mayer.debian.org Wed Jan 11 10:31:34 2012
Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -768,40 +821,38 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RMVmk-0001lH-Az
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:06 +0000
+ id 1RkvSw-00038L-4T
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:34 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RMVmj-0004an-9u
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:05 +0000
+ id 1RkvSu-00016Q-St
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:33 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RMVmc-00027v-M2
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:14:58 +0000
+ (envelope-from <buildd at mayer.debian.org>) id 1RkvSm-0004n8-Ac
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:24 +0000
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.15.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RMVmc-00027v-M2 at mayer.debian.org>
-Date: Sat, 05 Nov 2011 02:14:58 +0000
+Message-Id: <E1RkvSm-0004n8-Ac at mayer.debian.org>
+Date: Wed, 11 Jan 2012 10:31:24 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (mipsel) 05 Nov 2011 01:52 ║
+║ bedtools 2.15.0-1 (mipsel) 11 Jan 2012 10:11 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: mipsel
Hit http://debian.oregonstate.edu sid InRelease
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
@@ -809,6 +860,8 @@ Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
Hit http://debian.oregonstate.edu sid/main TranslationIndex
Ign http://debian.oregonstate.edu sid/contrib Translation-en
+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://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
@@ -816,12 +869,12 @@ Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [25.7 kB]
-Get:4 http://incoming.debian.org Packages [300 kB]
+Get:2 http://incoming.debian.org Release [1616 B]
+Get:3 http://incoming.debian.org Sources [47.8 kB]
+Get:4 http://incoming.debian.org Packages [552 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 328 kB in 2s (156 kB/s)
+Fetched 602 kB in 3s (196 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -842,11 +895,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (823 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 0s (6316 kB/s)
Download complete and in download only mode
Check arch
@@ -867,24 +920,24 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+ libpopt0 groff-base libpipeline1 gettext-base libunistring0 man-db html2text
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+ libpopt0 groff-base libpipeline1 gettext-base libunistring0 man-db html2text
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -892,121 +945,103 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
-zlib1g-dev: missing
+python: already installed (2.7.2-9)
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
+ diffstat gettext intltool-debian libcroco3 libffi5 libglib2.0-0 po-debconf
Suggested packages:
devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf quilt
- zlib1g-dev
+ cdbs debhelper diffstat gettext intltool-debian libcroco3 libffi5
+ libglib2.0-0 po-debconf quilt
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 16 newly installed, 0 to remove and 16 not upgraded.
-Need to get 0 B/6932 kB of archives.
-After this operation, 20.7 MB of additional disk space will be used.
+0 upgraded, 10 newly installed, 0 to remove and 41 not upgraded.
+Need to get 0 B/5314 kB of archives.
+After this operation, 13.8 MB of additional disk space will be used.
+Selecting previously unselected package libffi5.
+(Reading database ... 14500 files and directories currently installed.)
+Unpacking libffi5 (from .../libffi5_3.0.10-3_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
-(Reading database ... 11452 files and directories currently installed.)
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mipsel.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2_mipsel.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Processing triggers for man-db ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
-Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
+Setting up cdbs (0.4.100) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 asciidoc_8.6.6-1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 binutils-dev_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-3 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-2 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-10 libdb5.1_5.1.29-1 libdevmapper1.02.1_2:1.02.67-2 libdpkg-perl_1.16.1.1 libdw-dev_0.152-1+b1 libdw1_0.152-1+b1 libelf-dev_0.152-1+b1 libelf1_0.152-1+b1 libexpat1_2.0.1-7.2 libexpat1-dev_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 libgpg-error0_1.10-2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libnewt-dev_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libperl-dev_5.14.2-6 libperl5.14_5.14.2-6 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpopt0_1.16-3 libpython2.7_2.7.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libsqlite3-0_3.7.9-3 libss2_1.42~WIP-2011-10-16-1 libssl-dev_1.0.0e-2.1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_175-3 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 libxml2-utils_2.7.8.dfsg-5 libxslt1.1_1.1.26-8 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.2.8-11 python_2.7.2-9 python-dev_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-dev_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-2 udev_175-3 util-linux_2.19.1-5 xml-core_0.13 xmlto_0.0.23-2 xsltproc_1.1.26-8 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1017,12 +1052,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1033,24 +1068,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1063,21 +1098,21 @@ 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_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1110,41 +1145,50 @@ g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -1164,176 +1208,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -1372,28 +1412,29 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.14.3-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.15.0-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0214
+Build finished at 20120111-1031
-bedtools_2.14.3-1_mipsel.changes:
+bedtools_2.15.0-1_mipsel.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -1401,33 +1442,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- f3f67766afd0c131c5259c19600b7f435888623d 651142 bedtools_2.14.3-1_mipsel.deb
+ c269d51b5a5d5de03d017dd7ffdff85bdb3065c8 331704 bedtools_2.15.0-1_mipsel.deb
Checksums-Sha256:
- 083e81eaf94a1794d2110286acc43ef55d5ffe6ca2ba9920950c19d310220c35 651142 bedtools_2.14.3-1_mipsel.deb
+ c0390148a76602895228b854f257af4eb0cc4275426a3235ed43163eae716d38 331704 bedtools_2.15.0-1_mipsel.deb
Files:
- 84c4679dc2ee0dc60cd2848da9956fbd 651142 science optional bedtools_2.14.3-1_mipsel.deb
+ 0843ce5200d9df3b741d4f2ed819e888 331704 science optional bedtools_2.15.0-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_mipsel.deb
+bedtools_2.15.0-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 651142 bytes: control archive= 1769 bytes.
+ size 331704 bytes: control archive= 1867 bytes.
866 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5155
+ Installed-Size: 1344
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1443,7 +1487,7 @@ bedtools_2.14.3-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools_2.14.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools_2.15.0-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1457,50 +1501,40 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2*
- po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 16 to remove and 16 not upgraded.
-After this operation, 20.7 MB disk space will be freed.
-(Reading database ... 12413 files and directories currently installed.)
+ cdbs* debhelper* diffstat* gettext* intltool-debian* libcroco3* libffi5*
+ libglib2.0-0* po-debconf* quilt*
+0 upgraded, 0 newly installed, 10 to remove and 41 not upgraded.
+After this operation, 13.8 MB disk space will be freed.
+(Reading database ... 15361 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
-Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Removing libffi5 ...
+Purging configuration files for libffi5 ...
Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1508,19 +1542,19 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 104656
-Build-Time: 1211
+Build-Space: 67640
+Build-Time: 1119
Distribution: sid
-Install-Time: 44
-Job: bedtools_2.14.3-1
+Install-Time: 40
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1304
-Source-Version: 2.14.3-1
-Space: 104656
+Package-Time: 1191
+Source-Version: 2.15.0-1
+Space: 67640
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0214
-Build needed 00:21:44, 104656k disc space
+Finished at 20120111-1031
+Build needed 00:19:51, 67640k disc space
Signature with key 'B0903E66' requested:
diff --git a/mipsel.log b/mipsel.log
index d3895a2..a6dc714 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,4 +1,4 @@
-From buildd at mayer.debian.org Sat Nov 05 02:15:06 2011
+From buildd at mayer.debian.org Wed Jan 11 10:31:34 2012
Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,40 +6,38 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RMVmk-0001lH-Az
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:06 +0000
+ id 1RkvSw-00038L-4T
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:34 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RMVmj-0004an-9u
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:05 +0000
+ id 1RkvSu-00016Q-St
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:33 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RMVmc-00027v-M2
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:14:58 +0000
+ (envelope-from <buildd at mayer.debian.org>) id 1RkvSm-0004n8-Ac
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:24 +0000
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.15.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RMVmc-00027v-M2 at mayer.debian.org>
-Date: Sat, 05 Nov 2011 02:14:58 +0000
+Message-Id: <E1RkvSm-0004n8-Ac at mayer.debian.org>
+Date: Wed, 11 Jan 2012 10:31:24 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (mipsel) 05 Nov 2011 01:52 ║
+║ bedtools 2.15.0-1 (mipsel) 11 Jan 2012 10:11 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: mipsel
Hit http://debian.oregonstate.edu sid InRelease
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
@@ -47,6 +45,8 @@ Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
Hit http://debian.oregonstate.edu sid/main TranslationIndex
Ign http://debian.oregonstate.edu sid/contrib Translation-en
+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://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
@@ -54,12 +54,12 @@ Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [25.7 kB]
-Get:4 http://incoming.debian.org Packages [300 kB]
+Get:2 http://incoming.debian.org Release [1616 B]
+Get:3 http://incoming.debian.org Sources [47.8 kB]
+Get:4 http://incoming.debian.org Packages [552 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 328 kB in 2s (156 kB/s)
+Fetched 602 kB in 3s (196 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,11 +80,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (823 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 0s (6316 kB/s)
Download complete and in download only mode
Check arch
@@ -105,24 +105,24 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+ libpopt0 groff-base libpipeline1 gettext-base libunistring0 man-db html2text
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+ libpopt0 groff-base libpipeline1 gettext-base libunistring0 man-db html2text
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -130,121 +130,103 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
+diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
-zlib1g-dev: missing
+python: already installed (2.7.2-9)
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
+ diffstat gettext intltool-debian libcroco3 libffi5 libglib2.0-0 po-debconf
Suggested packages:
devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf quilt
- zlib1g-dev
+ cdbs debhelper diffstat gettext intltool-debian libcroco3 libffi5
+ libglib2.0-0 po-debconf quilt
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 16 newly installed, 0 to remove and 16 not upgraded.
-Need to get 0 B/6932 kB of archives.
-After this operation, 20.7 MB of additional disk space will be used.
+0 upgraded, 10 newly installed, 0 to remove and 41 not upgraded.
+Need to get 0 B/5314 kB of archives.
+After this operation, 13.8 MB of additional disk space will be used.
+Selecting previously unselected package libffi5.
+(Reading database ... 14500 files and directories currently installed.)
+Unpacking libffi5 (from .../libffi5_3.0.10-3_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
-(Reading database ... 11452 files and directories currently installed.)
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mipsel.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2_mipsel.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Processing triggers for man-db ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
-Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
+Setting up cdbs (0.4.100) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 asciidoc_8.6.6-1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 binutils-dev_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-3 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-2 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-10 libdb5.1_5.1.29-1 libdevmapper1.02.1_2:1.02.67-2 libdpkg-perl_1.16.1.1 libdw-dev_0.152-1+b1 libdw1_0.152-1+b1 libelf-dev_0.152-1+b1 libelf1_0.152-1+b1 libexpat1_2.0.1-7.2 libexpat1-dev_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 libgpg-error0_1.10-2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libnewt-dev_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libperl-dev_5.14.2-6 libperl5.14_5.14.2-6 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpopt0_1.16-3 libpython2.7_2.7.2-9 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libsqlite3-0_3.7.9-3 libss2_1.42~WIP-2011-10-16-1 libssl-dev_1.0.0e-2.1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_175-3 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 libxml2-utils_2.7.8.dfsg-5 libxslt1.1_1.1.26-8 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.2.8-11 python_2.7.2-9 python-dev_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-9 python2.7-dev_2.7.2-9 python2.7-minimal_2.7.2-9 quilt_0.50-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-2 udev_175-3 util-linux_2.19.1-5 xml-core_0.13 xmlto_0.0.23-2 xsltproc_1.1.26-8 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -255,12 +237,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -271,24 +253,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -301,21 +283,21 @@ 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_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -348,41 +330,50 @@ g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -402,176 +393,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -610,28 +597,29 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.14.3-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.15.0-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0214
+Build finished at 20120111-1031
-bedtools_2.14.3-1_mipsel.changes:
+bedtools_2.15.0-1_mipsel.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -639,33 +627,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- f3f67766afd0c131c5259c19600b7f435888623d 651142 bedtools_2.14.3-1_mipsel.deb
+ c269d51b5a5d5de03d017dd7ffdff85bdb3065c8 331704 bedtools_2.15.0-1_mipsel.deb
Checksums-Sha256:
- 083e81eaf94a1794d2110286acc43ef55d5ffe6ca2ba9920950c19d310220c35 651142 bedtools_2.14.3-1_mipsel.deb
+ c0390148a76602895228b854f257af4eb0cc4275426a3235ed43163eae716d38 331704 bedtools_2.15.0-1_mipsel.deb
Files:
- 84c4679dc2ee0dc60cd2848da9956fbd 651142 science optional bedtools_2.14.3-1_mipsel.deb
+ 0843ce5200d9df3b741d4f2ed819e888 331704 science optional bedtools_2.15.0-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_mipsel.deb
+bedtools_2.15.0-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 651142 bytes: control archive= 1769 bytes.
+ size 331704 bytes: control archive= 1867 bytes.
866 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5155
+ Installed-Size: 1344
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -681,7 +672,7 @@ bedtools_2.14.3-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools_2.14.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools_2.15.0-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -695,50 +686,40 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+The following package was automatically installed and is no longer required:
+ libpopt0
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2*
- po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 16 to remove and 16 not upgraded.
-After this operation, 20.7 MB disk space will be freed.
-(Reading database ... 12413 files and directories currently installed.)
+ cdbs* debhelper* diffstat* gettext* intltool-debian* libcroco3* libffi5*
+ libglib2.0-0* po-debconf* quilt*
+0 upgraded, 0 newly installed, 10 to remove and 41 not upgraded.
+After this operation, 13.8 MB disk space will be freed.
+(Reading database ... 15361 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
-Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Removing libffi5 ...
+Purging configuration files for libffi5 ...
Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -746,19 +727,19 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 104656
-Build-Time: 1211
+Build-Space: 67640
+Build-Time: 1119
Distribution: sid
-Install-Time: 44
-Job: bedtools_2.14.3-1
+Install-Time: 40
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1304
-Source-Version: 2.14.3-1
-Space: 104656
+Package-Time: 1191
+Source-Version: 2.15.0-1
+Space: 67640
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0214
-Build needed 00:21:44, 104656k disc space
+Finished at 20120111-1031
+Build needed 00:19:51, 67640k disc space
Signature with key 'B0903E66' requested:
diff --git a/powerpc.log b/powerpc.log
index 96f7fc3..f1765a9 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,68 @@
-From buildd at porpora.debian.org Sat Nov 05 02:00:27 2011
-Return-path: <buildd at porpora.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at praetorius.debian.org Wed Jan 11 07:15:30 2012
+Return-path: <buildd at praetorius.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RMVYZ-000891-Pr
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:27 +0000
-Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
- helo=porpora.debian.org)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1RksPC-0007Qk-Ae
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:15:30 +0000
+Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
+ (helo=praetorius.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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RMVYZ-0000c5-05; Sat, 05 Nov 2011 02:00:27 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1RMVYY-00056G-9c; Sat, 05 Nov 2011 02:00:26 +0000
-Message-Id: <E1RMVYY-00056G-9c at porpora.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 5 Nov 2011 02:00:26 +0000
-From: buildd on porpora <buildd at porpora.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on powerpc (dist=sid)
-Key-Id: 8CE75D05
+ CN=praetorius.debian.org,
+ EMAIL=hostmaster at praetorius.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1RksPB-0000it-B3; Wed, 11 Jan 2012 07:15:29 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1RksPA-0003s9-2m; Wed, 11 Jan 2012 07:15:28 +0000
+Date: Wed, 11 Jan 2012 07:15:28 +0000
+Message-Id: <E1RksPA-0003s9-2m at praetorius.debian.org>
+From: buildd on praetorius <buildd at praetorius.debian.org>
+To: wouter at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.15.0-1 on powerpc (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (powerpc) 05 Nov 2011 01:53 ║
+║ bedtools 2.15.0-1 (powerpc) 11 Jan 2012 07:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.uk.debian.org unstable/main Sources [5890 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
-Get:5 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
-Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [7704 kB]
+Get:1 http://ftp.se.debian.org unstable InRelease [189 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [6000 kB]
+Get:3 http://incoming.debian.org unstable InRelease [189 kB]
+Get:4 http://ftp.se.debian.org unstable/contrib Sources [54.4 kB]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [100 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [7853 kB]
+Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [55.3 kB]
+Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2085 B]
+Ign http://ftp.se.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.5 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:9 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5890 kB]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7704 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.5 kB]
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7853 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.3 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 [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.2 MB in 24s (1176 kB/s)
+Fetched 29.2 MB in 15s (1929 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +83,11 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 2s (454 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (495 kB/s)
Download complete and in download only mode
Check arch
@@ -102,132 +101,171 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 17 not upgraded.
-Need to get 9676 kB of archives.
-After this operation, 27.8 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-4 [37.2 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 37 not upgraded.
+Need to get 17.4 MB of archives.
+After this operation, 48.9 MB of additional disk space will be used.
+Get:1 http://ftp.se.debian.org/debian/ unstable/main libncursesw5 powerpc 5.9-4 [314 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-5 [37.6 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main libssl1.0.0 powerpc 1.0.0e-3 [1131 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.30.2-4 [1798 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5.1 [838 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main libexpat1 powerpc 2.0.1-7.2 [138 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main libdb4.8 powerpc 4.8.30-11 [694 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-3 [1014 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main libsqlite3-0 powerpc 3.7.9-2 [424 kB]
+Get:19 http://ftp.se.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.se.debian.org/debian/ unstable/main python2.7-minimal powerpc 2.7.2-10 [1745 kB]
+Get:21 http://ftp.se.debian.org/debian/ unstable/main python2.7 powerpc 2.7.2-10 [2613 kB]
+Get:22 http://ftp.se.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.se.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:26 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:27 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.se.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-2 [29.1 kB]
+Get:31 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://ftp.se.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 9676 kB in 1s (5904 kB/s)
+Fetched 17.4 MB in 1s (11.0 MB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10681 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_powerpc.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10725 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_powerpc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_powerpc.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_powerpc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_powerpc.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_powerpc.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_powerpc.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_powerpc.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_powerpc.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_powerpc.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_powerpc.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_powerpc.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_powerpc.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.09-2_powerpc.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_powerpc.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_powerpc.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_powerpc.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_powerpc.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously unselected package gettext.
@@ -235,49 +273,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_powerpc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_powerpc.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.4-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-1 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-1 g++-4.6_4.6.2-5 gcc_4:4.6.2-1 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.19.1-5 libbz2-1.0_1.0.6-1 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +338,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -304,24 +354,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -334,21 +384,21 @@ 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_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -381,41 +431,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -435,176 +494,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -643,62 +698,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.14.3-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.15.0-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0200
+Build finished at 20120111-0715
-bedtools_2.14.3-1_powerpc.changes:
+bedtools_2.15.0-1_powerpc.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 2566af9b100d3ce57600d80a171e4086c9121370 615234 bedtools_2.14.3-1_powerpc.deb
+ 3c8f2451061750c591d1b6ac3b5766f02099b26c 358462 bedtools_2.15.0-1_powerpc.deb
Checksums-Sha256:
- 9a63ca3bbad8479b781ab8b69169be3d7446b857860671b6ec3f31eed58171cf 615234 bedtools_2.14.3-1_powerpc.deb
+ 1aace34a32f960766fb5f963e9867a44cf900a58f984762a3bdf49eb47cf8dac 358462 bedtools_2.15.0-1_powerpc.deb
Files:
- e81ecddc44fffd56bdff51b2b214077d 615234 science optional bedtools_2.14.3-1_powerpc.deb
+ 00c345f6028f37fd21d951a267a61ef5 358462 science optional bedtools_2.15.0-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_powerpc.deb
+bedtools_2.15.0-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 615234 bytes: control archive= 1765 bytes.
+ size 358462 bytes: control archive= 1869 bytes.
867 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4988
+ Installed-Size: 1291
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -714,50 +773,54 @@ bedtools_2.14.3-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/bin/
--rwxr-xr-x root/root 149868 2011-11-05 02:00 ./usr/bin/nucBed
--rwxr-xr-x root/root 363104 2011-11-05 02:00 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113620 2011-11-05 02:00 ./usr/bin/mergeBed
--rwxr-xr-x root/root 145636 2011-11-05 02:00 ./usr/bin/sortBed
--rwxr-xr-x root/root 240116 2011-11-05 02:00 ./usr/bin/bedToBam
--rwxr-xr-x root/root 125164 2011-11-05 02:00 ./usr/bin/closestBed
--rwxr-xr-x root/root 314976 2011-11-05 02:00 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 109028 2011-11-05 02:00 ./usr/bin/annotateBed
--rwxr-xr-x root/root 149860 2011-11-05 02:00 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 111260 2011-11-05 02:00 ./usr/bin/complementBed
--rwxr-xr-x root/root 375408 2011-11-05 02:00 ./usr/bin/pairToBed
--rwxr-xr-x root/root 297552 2011-11-05 02:00 ./usr/bin/coverageBed
--rwxr-xr-x root/root 101012 2011-11-05 02:00 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 110100 2011-11-05 02:00 ./usr/bin/linksBed
--rwxr-xr-x root/root 110692 2011-11-05 02:00 ./usr/bin/slopBed
--rwxr-xr-x root/root 115588 2011-11-05 02:00 ./usr/bin/subtractBed
--rwxr-xr-x root/root 301656 2011-11-05 02:00 ./usr/bin/windowBed
--rwxr-xr-x root/root 235964 2011-11-05 02:00 ./usr/bin/bamToBed
--rwxr-xr-x root/root 289808 2011-11-05 02:00 ./usr/bin/tagBam
--rwxr-xr-x root/root 133996 2011-11-05 02:00 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 63772 2011-11-05 02:00 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 175244 2011-11-05 02:00 ./usr/bin/pairToPair
--rwxr-xr-x root/root 125204 2011-11-05 02:00 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 318048 2011-11-05 02:00 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 117732 2011-11-05 02:00 ./usr/bin/flankBed
--rwxr-xr-x root/root 146492 2011-11-05 02:00 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 114284 2011-11-05 02:00 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92940 2011-11-05 02:00 ./usr/bin/overlap
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 01:55 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/bin/
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 31 2012-01-11 07:15 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/complementBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/closestBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/slopBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/linksBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/sortBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/flankBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/tagBam
+-rwxr-xr-x root/root 1260664 2012-01-11 07:15 ./usr/bin/bedtools
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:11 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -771,7 +834,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-b6490ec3-a9d4-40ac-b508-aeb1b41839c2/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-3dd40f7d-d12c-4b29-9788-1661fd44b9aa/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -779,18 +842,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 107548
-Build-Time: 311
+Build-Space: 73016
+Build-Time: 255
Distribution: sid
-Install-Time: 44
-Job: bedtools_2.14.3-1
+Install-Time: 68
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 396
-Source-Version: 2.14.3-1
-Space: 107548
+Package-Time: 358
+Source-Version: 2.15.0-1
+Space: 73016
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0200
-Build needed 00:06:36, 107548k disc space
-Signature with key '8CE75D05' requested:
+Finished at 20120111-0715
+Build needed 00:05:58, 73016k disc space
+
diff --git a/s390.log b/s390.log
index 1494c28..044daa1 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Sat Nov 05 02:00:03 2011
-Return-path: <buildd at zandonai.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at zemlinsky.debian.org Wed Jan 11 07:12:45 2012
+Return-path: <buildd at zemlinsky.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RMVYB-00085h-PO
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:03 +0000
-Received: from zandonai.debian.org ([80.245.147.46])
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1RksMX-0007B4-Fz
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:12:45 +0000
+Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zandonai.debian.org,
- EMAIL=hostmaster at zandonai.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RMVYA-0000bb-Ku; Sat, 05 Nov 2011 02:00:02 +0000
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-Message-Id: <E1RMVY9-00015R-GA at zandonai.debian.org>
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
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MIME-Version: 1.0
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-Date: Sat, 5 Nov 2011 02:00:01 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
+Date: Wed, 11 Jan 2012 07:12:43 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on s390 (dist=sid)
-Key-Id: 772711F7
+Subject: Log for successful build of bedtools_2.15.0-1 on s390 (dist=sid)
+Key-Id: 1EEA506A
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (s390) 05 Nov 2011 01:56 ║
+║ bedtools 2.15.0-1 (s390) 11 Jan 2012 07:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: s390
-Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.de.debian.org unstable/main Sources [5890 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [189 kB]
+Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [5991 kB]
+Get:3 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [54.4 kB]
+Get:4 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [100 kB]
+Get:5 http://ftp-stud.hs-esslingen.de unstable/main s390 Packages [7742 kB]
+Get:6 http://incoming.debian.org unstable InRelease [189 kB]
+Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390 Packages [54.9 kB]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
+Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2085 B]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
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 [5890 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.9 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7615 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.5 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 [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7615 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.5 kB]
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7748 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.9 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 [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.1 MB in 29s (962 kB/s)
+Fetched 28.9 MB in 9s (3034 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 2s (432 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (625 kB/s)
Download complete and in download only mode
Check arch
@@ -102,132 +102,171 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.3)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-05-2)
-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 (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+debianutils: already installed (4.1)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.09)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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 (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.1)
+mount: already installed (2.20.1-1.1)
+util-linux: already installed (2.20.1-1.1)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 46 not upgraded.
-Need to get 9863 kB of archives.
-After this operation, 28.0 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-4 [38.9 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 libglib2.0-0 s390 2.28.8-1 [1681 kB]
-Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-5 [879 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-2 [122 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.09-2 [257 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main file s390 5.09-2 [52.6 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-5 [2073 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 17.7 MB of archives.
+After this operation, 49.5 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390 5.9-4 [323 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390 1.2.0-5 [39.0 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390 1.0.0e-3 [1223 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390 2.30.2-4 [1874 kB]
+Get:7 http://incoming.debian.org/debian/ unstable/main python2.7-minimal s390 2.7.2-10 [1695 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390 2.7.8.dfsg-5.1 [879 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390 0.6.2-2 [122 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390 2.0.1-7.2 [137 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390 4.8.30-11 [700 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390 2.6.0.2-3 [1029 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390 5.09-2 [257 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390 5.09-2 [52.6 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390 3.7.9-2 [450 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390 0.18.1.1-5 [2073 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390 1.55-2 [29.7 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+Get:32 http://incoming.debian.org/debian/ unstable/main python2.7 s390 2.7.2-10 [2655 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9863 kB in 2s (3829 kB/s)
+Fetched 17.7 MB in 2s (8525 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10720 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_s390.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10631 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_s390.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_s390.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_s390.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_s390.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_s390.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_s390.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_s390.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_s390.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously unselected package gettext.
@@ -235,49 +274,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_s390.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_s390.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-05-2 e2fsprogs_1.42~WIP-2011-10-05-2 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-05-2 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-6 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-05-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-10 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +339,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,30 +354,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,21 +385,21 @@ 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_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -371,7 +417,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -386,41 +432,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wfor
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -431,10 +486,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -444,176 +495,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -652,62 +699,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.14.3-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.15.0-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0159
+Build finished at 20120111-0712
-bedtools_2.14.3-1_s390.changes:
+bedtools_2.15.0-1_s390.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 9d67dfd763f71205f941761a89627915ab993a48 543134 bedtools_2.14.3-1_s390.deb
+ e32cd1b12422f648505c07d028c5b161091c6321 353440 bedtools_2.15.0-1_s390.deb
Checksums-Sha256:
- 5114b326bb1cbb5a946292f98051d59e86a74a427a628af61ac9e3c09f6b735b 543134 bedtools_2.14.3-1_s390.deb
+ f9d73fcfe29b096b4ad906a81f10b72067f97d97ea0e47520a4f736e23ba553d 353440 bedtools_2.15.0-1_s390.deb
Files:
- 3ae61fbf34fcdddb48566b809ac5cebb 543134 science optional bedtools_2.14.3-1_s390.deb
+ 22508ed00f7c81d9dff6a28707786112 353440 science optional bedtools_2.15.0-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_s390.deb
+bedtools_2.15.0-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 543134 bytes: control archive= 1758 bytes.
+ size 353440 bytes: control archive= 1871 bytes.
864 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4891
+ Installed-Size: 1252
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -723,50 +774,54 @@ bedtools_2.14.3-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/bin/
--rwxr-xr-x root/root 289044 2011-11-05 01:59 ./usr/bin/coverageBed
--rwxr-xr-x root/root 106140 2011-11-05 01:59 ./usr/bin/linksBed
--rwxr-xr-x root/root 293148 2011-11-05 01:59 ./usr/bin/windowBed
--rwxr-xr-x root/root 114056 2011-11-05 01:59 ./usr/bin/subtractBed
--rwxr-xr-x root/root 280868 2011-11-05 01:59 ./usr/bin/tagBam
--rwxr-xr-x root/root 116780 2011-11-05 01:59 ./usr/bin/flankBed
--rwxr-xr-x root/root 88724 2011-11-05 01:59 ./usr/bin/overlap
--rwxr-xr-x root/root 232524 2011-11-05 01:59 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109912 2011-11-05 01:59 ./usr/bin/complementBed
--rwxr-xr-x root/root 305840 2011-11-05 01:59 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 112724 2011-11-05 01:59 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 145548 2011-11-05 01:59 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63832 2011-11-05 01:59 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 371648 2011-11-05 01:59 ./usr/bin/pairToBed
--rwxr-xr-x root/root 235752 2011-11-05 01:59 ./usr/bin/bedToBam
--rwxr-xr-x root/root 97800 2011-11-05 01:59 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109472 2011-11-05 01:59 ./usr/bin/mergeBed
--rwxr-xr-x root/root 122412 2011-11-05 01:59 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 178220 2011-11-05 01:59 ./usr/bin/pairToPair
--rwxr-xr-x root/root 145500 2011-11-05 01:59 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 104652 2011-11-05 01:59 ./usr/bin/annotateBed
--rwxr-xr-x root/root 133196 2011-11-05 01:59 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 145560 2011-11-05 01:59 ./usr/bin/nucBed
--rwxr-xr-x root/root 122760 2011-11-05 01:59 ./usr/bin/closestBed
--rwxr-xr-x root/root 309532 2011-11-05 01:59 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 358696 2011-11-05 01:59 ./usr/bin/intersectBed
--rwxr-xr-x root/root 146224 2011-11-05 01:59 ./usr/bin/sortBed
--rwxr-xr-x root/root 108588 2011-11-05 01:59 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 01:57 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:09 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-01-11 07:12 ./usr/bin/
+-rwxr-xr-x root/root 36 2012-01-11 07:12 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 34 2012-01-11 07:12 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 29 2012-01-11 07:12 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1221576 2012-01-11 07:12 ./usr/bin/bedtools
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-01-11 07:12 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-01-11 07:12 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-01-11 07:12 ./usr/bin/flankBed
+-rwxr-xr-x root/root 35 2012-01-11 07:12 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 28 2012-01-11 07:12 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 31 2012-01-11 07:12 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-01-11 07:12 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-01-11 07:12 ./usr/bin/nucBed
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 32 2012-01-11 07:12 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-01-11 07:12 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-01-11 07:12 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 32 2012-01-11 07:12 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-01-11 07:12 ./usr/bin/complementBed
+-rwxr-xr-x root/root 30 2012-01-11 07:12 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-01-11 07:12 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 35 2012-01-11 07:12 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-01-11 07:12 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-01-11 07:12 ./usr/bin/tagBam
+-rwxr-xr-x root/root 35 2012-01-11 07:12 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:12 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 34 2012-01-11 07:12 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-01-11 07:12 ./usr/bin/unionBedGraphs
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -780,7 +835,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-4c46a11e-6346-4db3-b381-caefe0d5dd1c/build/buildd-bedtools_2.14.3-1-s390-fsMyKX
+Purging /var/lib/schroot/mount/sid-s390-sbuild-8e9a11ca-c237-49e8-9c2c-7ea133bf8333/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -788,87 +843,87 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 112288
-Build-Time: 169
+Build-Space: 77652
+Build-Time: 191
Distribution: sid
-Install-Time: 8
-Job: bedtools_2.14.3-1
+Install-Time: 20
+Job: bedtools_2.15.0-1
Package: bedtools
Package-Time: 227
-Source-Version: 2.14.3-1
-Space: 112288
+Source-Version: 2.15.0-1
+Space: 77652
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0159
-Build needed 00:03:47, 112288k disc space
-Signature with key '772711F7' requested:
-From buildd at zemlinsky.debian.org Sun Nov 27 04:20:02 2011
-Return-path: <buildd at zemlinsky.debian.org>
+Finished at 20120111-0712
+Build needed 00:03:47, 77652k disc space
+Signature with key '1EEA506A' requested:
+From buildd at zandonai.debian.org Wed Jan 11 07:15:44 2012
+Return-path: <buildd at zandonai.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
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+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
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+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
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+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
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+ id 1RksPO-0001Ag-Nj; Wed, 11 Jan 2012 07:15:42 +0000
+Message-Id: <E1RksPO-0001Ag-Nj 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: Sun, 27 Nov 2011 04:20:01 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+Date: Wed, 11 Jan 2012 07:15:42 +0000
+From: buildd on zandonai <buildd at zandonai.debian.org>
To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on s390x (dist=sid)
-Key-Id: B5D24954
+Subject: Log for successful build of bedtools_2.15.0-1 on s390x (dist=sid)
+Key-Id: 96C8554F
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (s390x) 27 Nov 2011 04:16 ║
+║ bedtools 2.15.0-1 (s390x) 11 Jan 2012 07:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: s390x
-Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [181 kB]
-Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [5921 kB]
-Get:3 http://incoming.debian.org unstable InRelease [181 kB]
-Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [56.5 kB]
-Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [103 kB]
-Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390x Packages [3917 kB]
-Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages [33.4 kB]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2045 B]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Get:1 http://ftp.de.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [6000 kB]
Ign http://incoming.debian.org InRelease
-Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5924 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main s390x Packages [4100 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390x Packages [33.4 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [54.4 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [100 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390x Packages [7090 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390x Packages [51.3 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2085 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main s390x Packages [7090 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390x Packages [51.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
Get:16 http://incoming.debian.org Release [1616 B]
-Get:17 http://incoming.debian.org Sources [32.6 kB]
-Get:18 http://incoming.debian.org Packages [1102 kB]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 21.8 MB in 6s (3290 kB/s)
+Fetched 27.6 MB in 25s (1088 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -886,13 +941,14 @@ 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 928 kB of source archives.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (6910 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (485 kB/s)
Download complete and in download only mode
Check arch
@@ -905,160 +961,210 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.2-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+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: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1+b1)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.11
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 3 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.0-5 [39.4 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4 [234 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3 [26.1 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4 [1866 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5 [890 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.2-2 [123 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5 [438 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 8.2.3 [213 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6 [1181 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.0.2-3 [1021 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.09-2 [253 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.09-2 [52.7 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5 [155 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15 [111 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5 [2157 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 8.9.11 [552 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.54-1 [29.2 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3 [199 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 17.9 MB of archives.
+After this operation, 51.2 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.0-5+b1 [39.8 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libssl1.0.0 s390x 1.0.0e-3 [1221 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4+b1 [1867 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5.1 [891 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.2-2+b1 [123 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 8.2.3+b1 [211 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.0.2-3+b1 [1029 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.09-2+b1 [252 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.09-2+b1 [52.9 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main libsqlite3-0 s390x 3.7.9-2 [443 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main python2.7-minimal s390x 2.7.2-10 [1742 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main python2.7 s390x 2.7.2-10 [2672 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:27 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:31 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3+b1 [199 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 0s (26.7 MB/s)
+Fetched 17.9 MB in 6s (2938 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10708 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10717 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390x.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_s390x.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390x.deb) ...
Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_s390x.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_s390x.deb) ...
+Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390x.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_s390x.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390x.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390x.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390x.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_s390x.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390x.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3+b1_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6+b1_s390x.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3+b1_s390x.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_s390x.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_s390x.deb) ...
+Unpacking file (from .../file_5.09-2+b1_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390x.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_s390x.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390x.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_s390x.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_s390x.deb) ...
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_s390x.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5+b1_s390x.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_s390x.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390x.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_s390x.deb) ...
+Setting up libncursesw5 (5.9-4+b1) ...
+Setting up libpipeline1 (1.2.0-5+b1) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpcre3 (8.12-4+b1) ...
+Setting up libffi5 (3.0.10-3+b1) ...
+Setting up libglib2.0-0 (2.30.2-4+b1) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
-Setting up libcroco3 (0.6.2-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
+Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libexpat1 (2.0.1-7.2) ...
+Setting up libunistring0 (0.9.3-5+b1) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up bsdmainutils (8.2.3+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up groff-base (1.21-6+b1) ...
+Setting up man-db (2.6.0.2-3+b1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
-Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up libmagic1 (5.09-2+b1) ...
+Setting up file (5.09-2+b1) ...
+Setting up gettext-base (0.18.1.1-5+b1) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up gettext (0.18.1.1-5+b1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.11) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
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 1 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.1-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.1-3 g++-4.6_4.6.2-5 gcc_4:4.6.1-3 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3+b1 bsdutils_1:2.20.1-1.1 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2+b1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.09 html2text_1.3.2a-15+b1 initscripts_2.88dsf-18 insserv_1.14.0-2.1+b1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2+b1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-4+b1 libgmp10_2:5.0.2+dfsg-2+b1 libgomp1_4.6.2-11 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.09-2+b1 libmount1_2.20.1-1.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-6+b1 libpam-modules-bin_1.1.3-6+b1 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6+b1 libpcre3_8.12-4+b1 libpipeline1_1.2.0-5+b1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4+b1 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3+b1 lsb-base_3.2-28 make_3.81-8.1+b1 man-db_2.6.0.2-3+b1 mawk_1.3.3-16+b1 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.4.2+svn3283-3+b1 patch_2.6.1-2+b1 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p1-2+b1 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.3.4.dfsg-3+b1 zlib1g-dev_1:1.2.3.4.dfsg-3+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1069,12 +1175,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1085,24 +1191,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1115,21 +1221,21 @@ 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_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1162,41 +1268,54 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)':
+src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
+src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -d lib ] || mkdir -p lib
[ -d include ] || mkdir -p include
[ -d include/api ] || mkdir -p include/api
[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
-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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -1216,176 +1335,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -1424,62 +1539,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.14.3-1_s390x.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.15.0-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111127-0419
+Build finished at 20120111-0715
-bedtools_2.14.3-1_s390x.changes:
+bedtools_2.15.0-1_s390x.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 25c2141d4ca508d380a476cfa004a06adb1a820e 694528 bedtools_2.14.3-1_s390x.deb
+ 9b44e0dc102233b93ada99aafbaf8d26c2b8f0cb 399096 bedtools_2.15.0-1_s390x.deb
Checksums-Sha256:
- b7097ca02edd72237d807cb86b673a0591b690212ccc797974004758ba705ff6 694528 bedtools_2.14.3-1_s390x.deb
+ 32136babe58c75e0ae6d7837a58199e48c7a5d4cea69ff4f966517ba34104558 399096 bedtools_2.15.0-1_s390x.deb
Files:
- 3f8a10e9c92162e105019acb895e5441 694528 science optional bedtools_2.14.3-1_s390x.deb
+ 5ba3774a3acd328ac007d5dcfa83f288 399096 science optional bedtools_2.15.0-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_s390x.deb
+bedtools_2.15.0-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 694528 bytes: control archive= 1759 bytes.
+ size 399096 bytes: control archive= 1867 bytes.
866 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5629
+ Installed-Size: 1436
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1495,50 +1614,54 @@ bedtools_2.14.3-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-27 04:16 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/bin/
--rwxr-xr-x root/root 105864 2011-11-27 04:19 ./usr/bin/overlap
--rwxr-xr-x root/root 422632 2011-11-27 04:19 ./usr/bin/pairToBed
--rwxr-xr-x root/root 261888 2011-11-27 04:19 ./usr/bin/bamToBed
--rwxr-xr-x root/root 126352 2011-11-27 04:19 ./usr/bin/slopBed
--rwxr-xr-x root/root 134488 2011-11-27 04:19 ./usr/bin/subtractBed
--rwxr-xr-x root/root 171344 2011-11-27 04:19 ./usr/bin/sortBed
--rwxr-xr-x root/root 348032 2011-11-27 04:19 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 135248 2011-11-27 04:19 ./usr/bin/flankBed
--rwxr-xr-x root/root 122920 2011-11-27 04:19 ./usr/bin/annotateBed
--rwxr-xr-x root/root 143048 2011-11-27 04:19 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 329400 2011-11-27 04:19 ./usr/bin/windowBed
--rwxr-xr-x root/root 168184 2011-11-27 04:19 ./usr/bin/nucBed
--rwxr-xr-x root/root 271480 2011-11-27 04:19 ./usr/bin/bedToBam
--rwxr-xr-x root/root 171600 2011-11-27 04:19 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 130408 2011-11-27 04:19 ./usr/bin/mergeBed
--rwxr-xr-x root/root 349576 2011-11-27 04:19 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 114880 2011-11-27 04:19 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 143256 2011-11-27 04:19 ./usr/bin/closestBed
--rwxr-xr-x root/root 130464 2011-11-27 04:19 ./usr/bin/complementBed
--rwxr-xr-x root/root 126336 2011-11-27 04:19 ./usr/bin/linksBed
--rwxr-xr-x root/root 134624 2011-11-27 04:19 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 208272 2011-11-27 04:19 ./usr/bin/pairToPair
--rwxr-xr-x root/root 155328 2011-11-27 04:19 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 317304 2011-11-27 04:19 ./usr/bin/tagBam
--rwxr-xr-x root/root 171504 2011-11-27 04:19 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 327512 2011-11-27 04:19 ./usr/bin/coverageBed
--rwxr-xr-x root/root 405624 2011-11-27 04:19 ./usr/bin/intersectBed
--rwxr-xr-x root/root 77224 2011-11-27 04:19 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/linksBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 31 2012-01-11 07:15 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/flankBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/complementBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 1409912 2012-01-11 07:15 ./usr/bin/bedtools
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/nucBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/closestBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/sortBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:10 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1552,7 +1675,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-77d51d80-d702-41d3-80db-5a13a750c941/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-76fe6f1a-ed8e-4ae9-b3a1-2c6ed418241d/sid-s390x-sbuild/build/buildd-bedtools_2.15.0-1-s390x-6s5uie
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1560,18 +1683,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 146144
-Build-Time: 201
+Build-Space: 108172
+Build-Time: 282
Distribution: sid
-Install-Time: 11
-Job: bedtools_2.14.3-1
+Install-Time: 18
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 221
-Source-Version: 2.14.3-1
-Space: 146144
+Package-Time: 344
+Source-Version: 2.15.0-1
+Space: 108172
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111127-0419
-Build needed 00:03:41, 146144k disc space
-Signature with key 'B5D24954' requested:
+Finished at 20120111-0715
+Build needed 00:05:44, 108172k disc space
+Signature with key '96C8554F' requested:
diff --git a/s390x.log b/s390x.log
index e46773d..b0a280a 100644
--- a/s390x.log
+++ b/s390x.log
@@ -1,69 +1,69 @@
-From buildd at zemlinsky.debian.org Sun Nov 27 04:20:02 2011
-Return-path: <buildd at zemlinsky.debian.org>
+From buildd at zandonai.debian.org Wed Jan 11 07:15:44 2012
+Return-path: <buildd at zandonai.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1RUWDi-0002Aw-8p
- for logs at buildd.debian.org; Sun, 27 Nov 2011 04:20:02 +0000
-Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1RksPP-0007Xc-Uz
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:15:44 +0000
+Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zemlinsky.debian.org,
- EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1RUWDh-0007uz-IR; Sun, 27 Nov 2011 04:20:01 +0000
-Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zemlinsky.debian.org>)
- id 1RUWDh-0007Jd-33; Sun, 27 Nov 2011 04:20:01 +0000
-Message-Id: <E1RUWDh-0007Jd-33 at zemlinsky.debian.org>
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1RksPP-0000rQ-6u; Wed, 11 Jan 2012 07:15:43 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1RksPO-0001Ag-Nj; Wed, 11 Jan 2012 07:15:42 +0000
+Message-Id: <E1RksPO-0001Ag-Nj 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: Sun, 27 Nov 2011 04:20:01 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+Date: Wed, 11 Jan 2012 07:15:42 +0000
+From: buildd on zandonai <buildd at zandonai.debian.org>
To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.3-1 on s390x (dist=sid)
-Key-Id: B5D24954
+Subject: Log for successful build of bedtools_2.15.0-1 on s390x (dist=sid)
+Key-Id: 96C8554F
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.3-1 (s390x) 27 Nov 2011 04:16 ║
+║ bedtools 2.15.0-1 (s390x) 11 Jan 2012 07:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: s390x
-Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [181 kB]
-Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [5921 kB]
-Get:3 http://incoming.debian.org unstable InRelease [181 kB]
-Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [56.5 kB]
-Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [103 kB]
-Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390x Packages [3917 kB]
-Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages [33.4 kB]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2045 B]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Get:1 http://ftp.de.debian.org unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [6000 kB]
Ign http://incoming.debian.org InRelease
-Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5924 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main s390x Packages [4100 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390x Packages [33.4 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [54.4 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [100 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390x Packages [7090 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390x Packages [51.3 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2085 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:13 http://incoming.debian.org unstable/main s390x Packages [7090 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390x Packages [51.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
Get:16 http://incoming.debian.org Release [1616 B]
-Get:17 http://incoming.debian.org Sources [32.6 kB]
-Get:18 http://incoming.debian.org Packages [1102 kB]
+Get:17 http://incoming.debian.org Sources [49.9 kB]
+Get:18 http://incoming.debian.org Packages [601 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 21.8 MB in 6s (3290 kB/s)
+Fetched 27.6 MB in 25s (1088 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 928 kB of source archives.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 0s (6910 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 1s (485 kB/s)
Download complete and in download only mode
Check arch
@@ -100,160 +101,210 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.2-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+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: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1+b1)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.11
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 3 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.0-5 [39.4 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4 [234 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3 [26.1 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4 [1866 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5 [890 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.2-2 [123 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5 [438 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 8.2.3 [213 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6 [1181 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.0.2-3 [1021 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.09-2 [253 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.09-2 [52.7 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5 [155 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15 [111 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5 [2157 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 8.9.11 [552 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.54-1 [29.2 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3 [199 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 17.9 MB of archives.
+After this operation, 51.2 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.0-5+b1 [39.8 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libssl1.0.0 s390x 1.0.0e-3 [1221 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4+b1 [1867 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5.1 [891 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.2-2+b1 [123 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 8.2.3+b1 [211 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.0.2-3+b1 [1029 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.09-2+b1 [252 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.09-2+b1 [52.9 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main libsqlite3-0 s390x 3.7.9-2 [443 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main python2.7-minimal s390x 2.7.2-10 [1742 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main python2.7 s390x 2.7.2-10 [2672 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:27 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:31 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3+b1 [199 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 0s (26.7 MB/s)
+Fetched 17.9 MB in 6s (2938 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10708 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10717 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390x.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_s390x.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390x.deb) ...
Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_s390x.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_s390x.deb) ...
+Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390x.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_s390x.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390x.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390x.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390x.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_s390x.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390x.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3+b1_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6+b1_s390x.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3+b1_s390x.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_s390x.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_s390x.deb) ...
+Unpacking file (from .../file_5.09-2+b1_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390x.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_s390x.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390x.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_s390x.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_s390x.deb) ...
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_s390x.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5+b1_s390x.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_s390x.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390x.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_s390x.deb) ...
+Setting up libncursesw5 (5.9-4+b1) ...
+Setting up libpipeline1 (1.2.0-5+b1) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpcre3 (8.12-4+b1) ...
+Setting up libffi5 (3.0.10-3+b1) ...
+Setting up libglib2.0-0 (2.30.2-4+b1) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
-Setting up libcroco3 (0.6.2-2) ...
-Setting up libunistring0 (0.9.3-5) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
+Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libexpat1 (2.0.1-7.2) ...
+Setting up libunistring0 (0.9.3-5+b1) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up bsdmainutils (8.2.3+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up groff-base (1.21-6+b1) ...
+Setting up man-db (2.6.0.2-3+b1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
-Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-5) ...
+Setting up libmagic1 (5.09-2+b1) ...
+Setting up file (5.09-2+b1) ...
+Setting up gettext-base (0.18.1.1-5+b1) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up gettext (0.18.1.1-5+b1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.11) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
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 1 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.1-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.1-3 g++-4.6_4.6.2-5 gcc_4:4.6.1-3 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_8.2.3+b1 bsdutils_1:2.20.1-1.1 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2+b1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.09 html2text_1.3.2a-15+b1 initscripts_2.88dsf-18 insserv_1.14.0-2.1+b1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2+b1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-4+b1 libgmp10_2:5.0.2+dfsg-2+b1 libgomp1_4.6.2-11 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.09-2+b1 libmount1_2.20.1-1.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-6+b1 libpam-modules-bin_1.1.3-6+b1 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6+b1 libpcre3_8.12-4+b1 libpipeline1_1.2.0-5+b1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4+b1 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3+b1 lsb-base_3.2-28 make_3.81-8.1+b1 man-db_2.6.0.2-3+b1 mawk_1.3.3-16+b1 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.4.2+svn3283-3+b1 patch_2.6.1-2+b1 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p1-2+b1 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.3.4.dfsg-3+b1 zlib1g-dev_1:1.2.3.4.dfsg-3+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,12 +315,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -280,24 +331,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -310,21 +361,21 @@ 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_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -357,41 +408,54 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)':
+src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
+src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -d lib ] || mkdir -p lib
[ -d include ] || mkdir -p include
[ -d include/api ] || mkdir -p include/api
[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
-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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -411,176 +475,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -619,62 +679,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.14.3-1_s390x.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.15.0-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111127-0419
+Build finished at 20120111-0715
-bedtools_2.14.3-1_s390x.changes:
+bedtools_2.15.0-1_s390x.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.14.3-1
+Version: 2.15.0-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 25c2141d4ca508d380a476cfa004a06adb1a820e 694528 bedtools_2.14.3-1_s390x.deb
+ 9b44e0dc102233b93ada99aafbaf8d26c2b8f0cb 399096 bedtools_2.15.0-1_s390x.deb
Checksums-Sha256:
- b7097ca02edd72237d807cb86b673a0591b690212ccc797974004758ba705ff6 694528 bedtools_2.14.3-1_s390x.deb
+ 32136babe58c75e0ae6d7837a58199e48c7a5d4cea69ff4f966517ba34104558 399096 bedtools_2.15.0-1_s390x.deb
Files:
- 3f8a10e9c92162e105019acb895e5441 694528 science optional bedtools_2.14.3-1_s390x.deb
+ 5ba3774a3acd328ac007d5dcfa83f288 399096 science optional bedtools_2.15.0-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_s390x.deb
+bedtools_2.15.0-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 694528 bytes: control archive= 1759 bytes.
+ size 399096 bytes: control archive= 1867 bytes.
866 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5629
+ Installed-Size: 1436
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -690,50 +754,54 @@ bedtools_2.14.3-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-27 04:16 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/bin/
--rwxr-xr-x root/root 105864 2011-11-27 04:19 ./usr/bin/overlap
--rwxr-xr-x root/root 422632 2011-11-27 04:19 ./usr/bin/pairToBed
--rwxr-xr-x root/root 261888 2011-11-27 04:19 ./usr/bin/bamToBed
--rwxr-xr-x root/root 126352 2011-11-27 04:19 ./usr/bin/slopBed
--rwxr-xr-x root/root 134488 2011-11-27 04:19 ./usr/bin/subtractBed
--rwxr-xr-x root/root 171344 2011-11-27 04:19 ./usr/bin/sortBed
--rwxr-xr-x root/root 348032 2011-11-27 04:19 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 135248 2011-11-27 04:19 ./usr/bin/flankBed
--rwxr-xr-x root/root 122920 2011-11-27 04:19 ./usr/bin/annotateBed
--rwxr-xr-x root/root 143048 2011-11-27 04:19 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 329400 2011-11-27 04:19 ./usr/bin/windowBed
--rwxr-xr-x root/root 168184 2011-11-27 04:19 ./usr/bin/nucBed
--rwxr-xr-x root/root 271480 2011-11-27 04:19 ./usr/bin/bedToBam
--rwxr-xr-x root/root 171600 2011-11-27 04:19 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 130408 2011-11-27 04:19 ./usr/bin/mergeBed
--rwxr-xr-x root/root 349576 2011-11-27 04:19 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 114880 2011-11-27 04:19 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 143256 2011-11-27 04:19 ./usr/bin/closestBed
--rwxr-xr-x root/root 130464 2011-11-27 04:19 ./usr/bin/complementBed
--rwxr-xr-x root/root 126336 2011-11-27 04:19 ./usr/bin/linksBed
--rwxr-xr-x root/root 134624 2011-11-27 04:19 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 208272 2011-11-27 04:19 ./usr/bin/pairToPair
--rwxr-xr-x root/root 155328 2011-11-27 04:19 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 317304 2011-11-27 04:19 ./usr/bin/tagBam
--rwxr-xr-x root/root 171504 2011-11-27 04:19 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 327512 2011-11-27 04:19 ./usr/bin/coverageBed
--rwxr-xr-x root/root 405624 2011-11-27 04:19 ./usr/bin/intersectBed
--rwxr-xr-x root/root 77224 2011-11-27 04:19 ./usr/bin/unionBedGraphs
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/linksBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 31 2012-01-11 07:15 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/flankBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/complementBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 1409912 2012-01-11 07:15 ./usr/bin/bedtools
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 36 2012-01-11 07:15 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-01-11 07:15 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-01-11 07:15 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-01-11 07:15 ./usr/bin/nucBed
+-rwxr-xr-x root/root 32 2012-01-11 07:15 ./usr/bin/closestBed
+-rwxr-xr-x root/root 33 2012-01-11 07:15 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 34 2012-01-11 07:15 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/sortBed
+-rwxr-xr-x root/root 29 2012-01-11 07:15 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:10 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:15 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -747,7 +815,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-77d51d80-d702-41d3-80db-5a13a750c941/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-76fe6f1a-ed8e-4ae9-b3a1-2c6ed418241d/sid-s390x-sbuild/build/buildd-bedtools_2.15.0-1-s390x-6s5uie
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -755,18 +823,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 146144
-Build-Time: 201
+Build-Space: 108172
+Build-Time: 282
Distribution: sid
-Install-Time: 11
-Job: bedtools_2.14.3-1
+Install-Time: 18
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 221
-Source-Version: 2.14.3-1
-Space: 146144
+Package-Time: 344
+Source-Version: 2.15.0-1
+Space: 108172
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111127-0419
-Build needed 00:03:41, 146144k disc space
-Signature with key 'B5D24954' requested:
+Finished at 20120111-0715
+Build needed 00:05:44, 108172k disc space
+Signature with key '96C8554F' requested:
diff --git a/sparc.log b/sparc.log
index 0413067..8f58ede 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,69 @@
-From buildd at spontini.debian.org Sat Nov 05 02:28:34 2011
-Return-path: <buildd at spontini.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at lebrun.debian.org Wed Jan 11 07:34:30 2012
+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=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 spontini.debian.org>)
- id 1RMVzE-0003ZS-Hf
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:28:03 +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 1Rksha-0002pC-2G
+ for logs at buildd.debian.org; Wed, 11 Jan 2012 07:34:30 +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)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
- id 1RMVzD-0005Aw-FC
- for logs at buildd.debian.org; Sat, 05 Nov 2011 02:27:59 +0000
-Received: from buildd by spontini.debian.org with local (Exim 4.72)
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-Message-Id: <E1RMVz8-0001wt-TX at spontini.debian.org>
+ 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 lebrun.debian.org>)
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+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1RkshV-0004dN-7L; Wed, 11 Jan 2012 07:34:25 +0000
+Message-Id: <E1RkshV-0004dN-7L 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: Sat, 5 Nov 2011 02:27:54 +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_2.14.3-1 on sparc (dist=sid)
-Key-Id: 0D4C040C
+Date: Wed, 11 Jan 2012 07:34:25 +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_2.15.0-1 on sparc (dist=sid)
+Key-Id: 4DF860F5
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 2.14.3-1 (sparc) 05 Nov 2011 01:57 ║
+║ bedtools 2.15.0-1 (sparc) 11 Jan 2012 07:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.3-1
-Source Version: 2.14.3-1
+Version: 2.15.0-1
+Source Version: 2.15.0-1
Architecture: sparc
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [189 kB]
+Get:2 http://incoming.debian.org unstable InRelease [189 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [6000 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [54.4 kB]
+Get:5 http://debian.carnet.hr unstable/non-free Sources [100 kB]
Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1604 B]
-Get:5 http://mirror-ubc.debian.org unstable/main Sources [5890 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5890 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [56.9 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main sparc Packages [7653 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib sparc Packages [55.4 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7653 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.4 kB]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://debian.carnet.hr unstable/main sparc Packages [7791 kB]
+Get:8 http://incoming.debian.org Release [1616 B]
+Get:9 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.0 kB]
+Ign http://debian.carnet.hr unstable/contrib TranslationIndex
+Get:11 http://debian.carnet.hr unstable/main TranslationIndex [2085 B]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [100 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7791 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [25.7 kB]
-Get:18 http://incoming.debian.org Packages [300 kB]
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2085 B]
+Get:17 http://incoming.debian.org Sources [50.2 kB]
+Get:18 http://incoming.debian.org Packages [591 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.1 MB in 1min 4s (436 kB/s)
+Fetched 29.0 MB in 32s (900 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
-Fetched 928 kB in 1s (543 kB/s)
+Need to get 969 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (tar) [963 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.15.0-1 (diff) [4499 B]
+Fetched 969 kB in 2s (431 kB/s)
Download complete and in download only mode
Check arch
@@ -103,133 +102,172 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, 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
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
+debianutils: already installed (4.1)
diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
-findutils: already installed (4.4.2-1+b2)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42-1)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.10-1)
+gzip: already installed (1.4-2)
+hostname: already installed (3.09)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-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 (2.13-21)
-libc6-dev-sparc64: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+sysvinit-utils: already installed (2.88dsf-18)
+sysvinit: already installed (2.88dsf-18)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.1)
+mount: already installed (2.20.1-1.1)
+util-linux: already installed (2.20.1-1.1)
+libc6-dev: already installed (2.13-24)
+libc6-dev-sparc64: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.9
+Using default version 8.9.14
quilt: missing
+python: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0
+ libxml2 man-db mime-support po-debconf python-minimal python2.7
+ python2.7-minimal
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ www-browser libmail-box-perl python-doc python-tk python2.7-doc
+ binfmt-support procmail graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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 20 not upgraded.
-Need to get 9454 kB of archives.
-After this operation, 27.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-4 [34.9 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
-Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 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 0.48-8 [357 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+ html2text intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0
+ libmagic1 libncursesw5 libpcre3 libpipeline1 libsqlite3-0 libssl1.0.0
+ libunistring0 libxml2 man-db mime-support po-debconf python python-minimal
+ python2.7 python2.7-minimal quilt zlib1g-dev
+0 upgraded, 32 newly installed, 0 to remove and 1 not upgraded.
+Need to get 16.8 MB of archives.
+After this operation, 47.8 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libncursesw5 sparc 5.9-4 [302 kB]
+Get:2 http://incoming.debian.org/buildd-unstable/ python2.7-minimal 2.7.2-10 [1598 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-5 [35.0 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main libssl1.0.0 sparc 1.0.0e-3 [1047 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.30.2-4 [1693 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5.1 [816 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
+Get:10 http://incoming.debian.org/buildd-unstable/ python2.7 2.7.2-10 [2582 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libexpat1 sparc 2.0.1-7.2 [128 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libdb4.8 sparc 4.8.30-11 [639 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-3 [997 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main libsqlite3-0 sparc 3.7.9-2 [400 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main mime-support all 3.51-1 [35.0 kB]
+Get:22 http://debian.carnet.hr/debian/ unstable/main python-minimal all 2.7.2-9 [39.8 kB]
+Get:23 http://debian.carnet.hr/debian/ unstable/main python all 2.7.2-9 [176 kB]
+Get:24 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.100 [77.1 kB]
+Get:25 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:26 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
+Get:27 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:30 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-2 [28.4 kB]
+Get:31 http://debian.carnet.hr/debian/ unstable/main quilt all 0.50-2 [381 kB]
+Get:32 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 9454 kB in 2s (3528 kB/s)
+Fetched 16.8 MB in 12s (1361 kB/s)
+Selecting previously unselected package libncursesw5.
+(Reading database ... 10998 files and directories currently installed.)
+Unpacking libncursesw5 (from .../libncursesw5_5.9-4_sparc.deb) ...
Selecting previously unselected package libpipeline1.
-(Reading database ... 10913 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_sparc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_sparc.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_sparc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_sparc.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_sparc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_sparc.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_sparc.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_sparc.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_sparc.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_sparc.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_sparc.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_sparc.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_sparc.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.09-2_sparc.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_sparc.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_sparc.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_sparc.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.2-10_sparc.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-9_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously unselected package gettext.
@@ -237,49 +275,61 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_sparc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
+Unpacking diffstat (from .../diffstat_1.55-2_sparc.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Setting up libncursesw5 (5.9-4) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libssl1.0.0 (1.0.0e-3) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-5.1) ...
Setting up libcroco3 (0.6.2-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
Setting up bsdmainutils (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 man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up cdbs (0.4.99) ...
+Setting up libsqlite3-0 (3.7.9-2) ...
+Setting up mime-support (3.51-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.2-10) ...
+Setting up python2.7 (2.7.2-10) ...
+Setting up python-minimal (2.7.2-9) ...
+Setting up python (2.7.2-9) ...
+Setting up cdbs (0.4.100) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.9) ...
-Setting up diffstat (1.54-1) ...
-Setting up quilt (0.48-8) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (8.9.14) ...
+Setting up diffstat (1.55-2) ...
+Setting up quilt (0.50-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 libc6-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gcc_4:4.6.1-3 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 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_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.1.6-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.100 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libc6-dev-sparc64_2.13-24 libc6-sparc64_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libsqlite3-0_3.7.9-2 libss2_1.42-1 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 linux-libc-dev_3.1.6-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mime-support_3.51-1 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-9 python-minimal_2.7.2-9 python2.7_2.7.2-10 python2.7-minimal_2.7.2-10 quilt_0.50-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -290,12 +340,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.3
-dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.15.0-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.15.0
+dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -306,24 +356,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.3-1
- dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: source version 2.15.0-1
+ dpkg-source --before-build bedtools-2.15.0
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -336,21 +386,21 @@ 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_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -383,41 +433,50 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* 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 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
+ * compiling BamAlignment.cpp
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamDeviceFactory_p.cpp
+ * compiling BamFile_p.cpp
+ * compiling BamFtp_p.cpp
+ * compiling BamHttp_p.cpp
+ * compiling BamPipe_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling ByteArray_p.cpp
+ * compiling HostAddress_p.cpp
+ * compiling HostInfo_p.cpp
+ * compiling HttpHeader_p.cpp
+ * compiling ILocalIODevice_p.cpp
+ * compiling RollingBuffer_p.cpp
+ * compiling TcpSocketEngine_p.cpp
+ * compiling TcpSocketEngine_unix_p.cpp
+ * compiling TcpSocket_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+ * compiling BamException_p.cpp
[ -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
+ * 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/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
@@ -437,176 +496,172 @@ genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-
- Building in src/annotateBed
* compiling annotateMain.cpp
-annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
- * 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
+bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
+bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- Building in src/bedToBam
* compiling bedToBam.cpp
-bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * linking bedToBam
+
+- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
+bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
+bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- Building in src/bedToIgv
* compiling bedToIgv.cpp
- * linking bedToIgv
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
- * linking bed12ToBed6
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
- * linking closestBed
+
+- Building in src/clusterBed
+ * compiling clusterMain.cpp
+clusterMain.cpp: In function 'int cluster_main(int, char**)':
+clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling clusterBed.cpp
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
- * linking complementBed
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
- * linking coverageBed
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
- * linking fastaFromBed
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
- * linking flankBed
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
- * linking genomeCoverageBed
+
+- Building in src/getOverlap
+ * compiling getOverlap.cpp
+getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
+getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+
+- Building in src/groupBy
+ * compiling groupBy.cpp
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
- * linking intersectBed
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
- * linking linksBed
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
- * linking maskFastaFromBed
- Building in src/mergeBed
* compiling mergeMain.cpp
-mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
- * linking mergeBed
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
-multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
- * linking multiBamCov
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp: In function 'int main(int, char**)':
-multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
-multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking multiIntersectBed
+multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
+multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- 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: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * linking pairToBed
- Building in src/pairToPair
* compiling pairToPairMain.cpp
-pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling 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
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
- * linking shuffleBed
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
- * linking slopBed
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
- * linking sortBed
- Building in src/subtractBed
* compiling subtractMain.cpp
-subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
- * linking subtractBed
- Building in src/tagBam
* compiling tagBamMain.cpp
-tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
- * linking tagBam
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
-unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * linking unionBedGraphs
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
- * linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+- Building in src/windowMaker
+ * compiling windowMakerMain.cpp
+ * compiling windowMaker.cpp
+
+- Building main bedtools binary.
+done.
+- Creating executables for old CLI.
+done.
+make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -645,62 +700,66 @@ dh_strip -pbedtools
dh_compress -pbedtools
dh_fixperms -pbedtools
dh_makeshlibs -pbedtools
+rm /build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (spontini) <buildd_sparc-spontini at buildd.debian.org> >../bedtools_2.14.3-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.15.0-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.3
+ dpkg-source --after-build bedtools-2.15.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111105-0227
+Build finished at 20120111-0734
-bedtools_2.14.3-1_sparc.changes:
+bedtools_2.15.0-1_sparc.changes:
Format: 1.8
-Date: Fri, 04 Nov 2011 09:25:38 +0900
+Date: Wed, 11 Jan 2012 15:07:45 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.14.3-1
+Version: 2.15.0-1
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
Changes:
- bedtools (2.14.3-1) unstable; urgency=low
+ bedtools (2.15.0-1) unstable; urgency=low
.
- [04f6aa3] Bugfix release.
+ [3f8e754] Upstream version 2.15.0.
+ [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
+ [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
+ distributed by the filo package.
Checksums-Sha1:
- 875ab669db90062d342af236009f54c575b5ba2e 587132 bedtools_2.14.3-1_sparc.deb
+ d59c2b3055958af646c1578ed97f249f89a8df57 337630 bedtools_2.15.0-1_sparc.deb
Checksums-Sha256:
- 7e2c91cf09451a4198cf79aa4fc0abff36f7db60fc2be2cca47198ff1a9e19fb 587132 bedtools_2.14.3-1_sparc.deb
+ 1d5d08e93c70bba215e7f10da98f6eea75466268226643b3c779a63d66c5a55a 337630 bedtools_2.15.0-1_sparc.deb
Files:
- bd4a759944dd5c0c1c556fcef8cef218 587132 science optional bedtools_2.14.3-1_sparc.deb
+ fc953b9d329a1e40fbaf2b5f4afc2b47 337630 science optional bedtools_2.15.0-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.3-1_sparc.deb
+bedtools_2.15.0-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 587132 bytes: control archive= 1767 bytes.
+ size 337630 bytes: control archive= 1865 bytes.
865 bytes, 19 lines control
- 2085 bytes, 36 lines md5sums
+ 2299 bytes, 40 lines md5sums
Package: bedtools
- Version: 2.14.3-1
+ Version: 2.15.0-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4722
+ Installed-Size: 1289
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -716,50 +775,54 @@ bedtools_2.14.3-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-05 02:01 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/bin/
--rwxr-xr-x root/root 143908 2011-11-05 02:26 ./usr/bin/sortBed
--rwxr-xr-x root/root 84868 2011-11-05 02:26 ./usr/bin/overlap
--rwxr-xr-x root/root 105968 2011-11-05 02:26 ./usr/bin/mergeBed
--rwxr-xr-x root/root 277964 2011-11-05 02:26 ./usr/bin/coverageBed
--rwxr-xr-x root/root 293276 2011-11-05 02:26 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 93984 2011-11-05 02:26 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 103204 2011-11-05 02:26 ./usr/bin/complementBed
--rwxr-xr-x root/root 364188 2011-11-05 02:26 ./usr/bin/pairToBed
--rwxr-xr-x root/root 109848 2011-11-05 02:26 ./usr/bin/subtractBed
--rwxr-xr-x root/root 110508 2011-11-05 02:26 ./usr/bin/flankBed
--rwxr-xr-x root/root 175004 2011-11-05 02:26 ./usr/bin/pairToPair
--rwxr-xr-x root/root 136940 2011-11-05 02:26 ./usr/bin/multiIntersectBed
--rwxr-xr-x root/root 60340 2011-11-05 02:26 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 109568 2011-11-05 02:26 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 347776 2011-11-05 02:26 ./usr/bin/intersectBed
--rwxr-xr-x root/root 274036 2011-11-05 02:26 ./usr/bin/tagBam
--rwxr-xr-x root/root 118900 2011-11-05 02:26 ./usr/bin/closestBed
--rwxr-xr-x root/root 224720 2011-11-05 02:26 ./usr/bin/bamToBed
--rwxr-xr-x root/root 139536 2011-11-05 02:26 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 102632 2011-11-05 02:26 ./usr/bin/slopBed
--rwxr-xr-x root/root 127360 2011-11-05 02:26 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 117776 2011-11-05 02:26 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 298604 2011-11-05 02:26 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142564 2011-11-05 02:26 ./usr/bin/nucBed
--rwxr-xr-x root/root 101500 2011-11-05 02:26 ./usr/bin/annotateBed
--rwxr-xr-x root/root 104044 2011-11-05 02:26 ./usr/bin/linksBed
--rwxr-xr-x root/root 224712 2011-11-05 02:26 ./usr/bin/bedToBam
--rwxr-xr-x root/root 282188 2011-11-05 02:26 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-01-11 07:33 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 34 2012-01-11 07:33 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 35 2012-01-11 07:33 ./usr/bin/complementBed
+-rwxr-xr-x root/root 1258696 2012-01-11 07:33 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-01-11 07:33 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-01-11 07:33 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 28 2012-01-11 07:33 ./usr/bin/tagBam
+-rwxr-xr-x root/root 28 2012-01-11 07:33 ./usr/bin/nucBed
+-rwxr-xr-x root/root 31 2012-01-11 07:33 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 34 2012-01-11 07:33 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 35 2012-01-11 07:33 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 34 2012-01-11 07:33 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 34 2012-01-11 07:33 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 29 2012-01-11 07:33 ./usr/bin/slopBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-01-11 07:33 ./usr/bin/closestBed
+-rwxr-xr-x root/root 30 2012-01-11 07:33 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-01-11 07:33 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 34 2012-01-11 07:33 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 36 2012-01-11 07:33 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 32 2012-01-11 07:33 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 32 2012-01-11 07:33 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 30 2012-01-11 07:33 ./usr/bin/linksBed
+-rwxr-xr-x root/root 35 2012-01-11 07:33 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 29 2012-01-11 07:33 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 30 2012-01-11 07:33 ./usr/bin/flankBed
+-rwxr-xr-x root/root 33 2012-01-11 07:33 ./usr/bin/bedToBam
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-01-11 07:23 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-01-02 10:51 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-01-02 10:51 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-11 07:33 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2012-01-02 10:51 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2012-01-05 01:53 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-01-02 10:51 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 832 2012-01-11 06:08 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -773,7 +836,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-e63feb8a-788a-4423-bcb4-9ab130d2897d/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-3e46963f-c9b5-4f65-adcc-b0d16c602978/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -781,18 +844,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 104408
-Build-Time: 1596
+Build-Space: 70120
+Build-Time: 614
Distribution: sid
-Install-Time: 83
-Job: bedtools_2.14.3-1
+Install-Time: 99
+Job: bedtools_2.15.0-1
Package: bedtools
-Package-Time: 1789
-Source-Version: 2.14.3-1
-Space: 104408
+Package-Time: 768
+Source-Version: 2.15.0-1
+Space: 70120
Status: successful
-Version: 2.14.3-1
+Version: 2.15.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111105-0227
-Build needed 00:29:49, 104408k disc space
-Signature with key '0D4C040C' requested:
+Finished at 20120111-0734
+Build needed 00:12:48, 70120k disc space
+Signature with key '4DF860F5' requested:
--
Suite of utilities for comparing genomic features.
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