[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.15.0-1-2-g2a2605e
Charles Plessy
plessy at debian.org
Sat Mar 17 02:44:28 UTC 2012
The following commit has been merged in the meta branch:
commit 2a2605ec3744a9b84b4b9dc8697acb4baa13ecaa
Author: Charles Plessy <plessy at debian.org>
Date: Sat Mar 17 11:43:57 2012 +0900
Build logs for 2.16.1-1.
diff --git a/armel.log b/armel.log
index b73438f..76ac3c9 100644
--- a/armel.log
+++ b/armel.log
@@ -1,68 +1,69 @@
-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])
+From buildd at alwyn.debian.org Fri Mar 16 12:54:47 2012
+Return-path: <buildd at alwyn.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- 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 antheil.debian.org>)
- id 1RktxJ-0008Pz-BD
- 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)
+ (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
+ id 1S8WgB-0002eu-3F
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:54:47 +0000
+Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=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 antheil.debian.org>)
- id 1RktxH-0007pJ-29
- for logs at buildd.debian.org; Wed, 11 Jan 2012 08:54:47 +0000
-Received: from buildd by antheil.debian.org with local (Exim 4.72)
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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)
+ CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
+ id 1S8WgA-0007mi-66
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:54:46 +0000
+Received: from buildd by alwyn.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alwyn.debian.org>)
+ id 1S8Wg8-0003QC-MV; Fri, 16 Mar 2012 12:54:44 +0000
+Date: Fri, 16 Mar 2012 12:54:44 +0000
+Message-Id: <E1S8Wg8-0003QC-MV at alwyn.debian.org>
+From: buildd on alwyn <buildd at alwyn.debian.org>
+To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.16.1-1 on armel (dist=sid)
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 antheil.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alwyn.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (armel) 11 Jan 2012 08:27 ║
+║ bedtools 2.16.1-1 (armel) 16 Mar 2012 12:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: armel
-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]
+Get:1 http://ftp.uk.debian.org unstable InRelease [198 kB]
+Get:2 http://incoming.debian.org unstable InRelease [198 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6213 kB]
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 [6000 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6213 kB]
Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [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]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.8 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [5770 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armel Packages [36.9 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2085 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib armel Packages [55.0 kB]
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2223 B]
+Get:11 http://ftp.uk.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:12 http://ftp.uk.debian.org unstable/main Translation-en [3902 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main armel Packages [5770 kB]
+Get:16 http://incoming.debian.org unstable/contrib armel Packages [36.9 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [59.8 kB]
+Get:22 http://incoming.debian.org Packages [692 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 29.0 MB in 1min 6s (439 kB/s)
+Fetched 33.4 MB in 1min 19s (421 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (858 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,33 +127,33 @@ base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
+debianutils: already installed (4.2.1)
diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.2)
e2fsprogs: already installed (1.42-1)
-findutils: already installed (4.4.2-1+b1)
+findutils: already installed (4.4.2-4)
grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.08)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-7)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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 (2.13-24)
-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)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-26)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -166,7 +167,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -180,60 +181,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 48 not upgraded.
+Need to get 17.0 MB of archives.
+After this operation, 46.4 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main zlib1g armel 1:1.2.6.dfsg-2 [85.4 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armel 5.9-4 [303 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.1-1 [34.9 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armel 1.0.0h-1 [1013 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.10-1 [250 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.30.2-6 [1744 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-7 [818 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.4-2 [140 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armel 2.0.1-7.2 [114 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armel 4.8.30-11 [622 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.1 [208 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.1-1 [1030 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.10-1 [52.7 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armel 3.7.10-1 [400 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armel 2.7.3~rc1-1 [1660 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armel 2.7.3~rc1-1 [2696 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-2 [28.5 kB]
+Get:32 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.6.dfsg-2 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 16.6 MB in 4s (3461 kB/s)
+Fetched 17.0 MB in 4s (3539 kB/s)
+(Reading database ... 10578 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_armel.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10565 files and directories currently installed.)
+(Reading database ... 10578 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_armel.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armel.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_armel.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_armel.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_armel.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_armel.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_armel.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_armel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_armel.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_armel.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armel.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_armel.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_armel.deb) ...
Selecting previously unselected package libunistring0.
@@ -241,31 +251,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_armel.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_armel.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_armel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_armel.deb) ...
+Unpacking file (from .../archives/file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_armel.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_armel.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_armel.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_armel.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_armel.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously unselected package gettext.
@@ -275,59 +283,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_armel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armel.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-3) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 24 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.2-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgomp1_4.6.2-12 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.2-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -338,12 +346,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -354,24 +362,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -384,52 +406,44 @@ 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_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -469,143 +483,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -614,59 +623,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -674,6 +681,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -681,84 +694,156 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-armel-XxZntt/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-armel-ZNjsRq/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../bedtools_2.15.0-1_armel.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org> >../bedtools_2.16.1-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0854
+Build finished at 20120316-1254
-bedtools_2.15.0-1_armel.changes:
+bedtools_2.16.1-1_armel.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
+Maintainer: armel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- e6e1417713a2d3faab139338fdd43a86b0b2828e 333406 bedtools_2.15.0-1_armel.deb
+ 89b66d65305953d366019ae678a1e1c41bb82185 366444 bedtools_2.16.1-1_armel.deb
Checksums-Sha256:
- 47d37c342c7df5e01ac02af7c01390e884fbe2c2092ea8b9cbd05a8c81af4965 333406 bedtools_2.15.0-1_armel.deb
+ eec185a1183a74a23e74057d503c3377263eb192e2206b0b19078e3f9f9f773b 366444 bedtools_2.16.1-1_armel.deb
Files:
- 30a6b0459b3d6b804a38a2fc3fde6f7d 333406 science optional bedtools_2.15.0-1_armel.deb
+ 10445aad88a29b4a3c0401a89cdf7e70 366444 science optional bedtools_2.16.1-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_armel.deb
+bedtools_2.16.1-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 333406 bytes: control archive= 1869 bytes.
+ size 366444 bytes: control archive= 1976 bytes.
865 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1092
+ Installed-Size: 1206
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -774,54 +859,58 @@ bedtools_2.15.0-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-03-16 12:54 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 29 2012-03-16 12:53 ./usr/bin/sortBed
+-rwxr-xr-x root/root 36 2012-03-16 12:53 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 31 2012-03-16 12:53 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 31 2012-03-16 12:53 ./usr/bin/randomBed
+-rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/complementBed
+-rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/nucBed
+-rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/flankBed
+-rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/closestBed
+-rwxr-xr-x root/root 30 2012-03-16 12:53 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/tagBam
+-rwxr-xr-x root/root 28 2012-03-16 12:53 ./usr/bin/mapBed
+-rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 1173824 2012-03-16 12:54 ./usr/bin/bedtools
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 36 2012-03-16 12:53 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 32 2012-03-16 12:53 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-03-16 12:53 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 33 2012-03-16 12:53 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 29 2012-03-16 12:53 ./usr/bin/slopBed
+-rwxr-xr-x root/root 34 2012-03-16 12:53 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 31 2012-03-16 12:53 ./usr/bin/expandCols
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -835,7 +924,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-60302bc7-fb58-4465-91b9-d135480d3f69/build/buildd-bedtools_2.15.0-1-armel-XxZntt
+Purging /var/lib/schroot/mount/sid-armel-sbuild-86ea2b95-2c30-479d-b5b9-37e46d2328ad/build/buildd-bedtools_2.16.1-1-armel-ZNjsRq
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -843,19 +932,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 65992
-Build-Time: 1374
+Build-Space: 75596
+Build-Time: 1701
Distribution: sid
-Install-Time: 142
-Job: bedtools_2.15.0-1
+Install-Time: 160
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 1615
-Source-Version: 2.15.0-1
-Space: 65992
+Package-Time: 1981
+Source-Version: 2.16.1-1
+Space: 75596
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0854
-Build needed 00:26:55, 65992k disc space
-Signature with key '5EAEB276' requested:
+Finished at 20120316-1254
+Build needed 00:33:01, 75596k disc space
+Signature with key '4CB559DB' requested:
diff --git a/armhf.log b/armhf.log
index b50b33f..54a1db3 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,67 +1,69 @@
-From buildd at hummel.debian.org Wed Jan 11 07:33:42 2012
-Return-path: <buildd at hummel.debian.org>
+From buildd at hasse.debian.org Fri Mar 16 14:04:16 2012
+Return-path: <buildd at hasse.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 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)
+ (Exim 4.72) (envelope-from <buildd at hasse.debian.org>)
+ id 1S8XlP-0005R2-S1
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 14:04:16 +0000
+Received: from [217.140.96.68] (helo=hasse.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=hummel.debian.org, EMAIL=hostmaster at hummel.debian.org (verified)
+ CN=hasse.debian.org, EMAIL=hostmaster at hasse.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)
+ (Exim 4.72) (envelope-from <buildd at hasse.debian.org>)
+ id 1S8XlO-0004Wn-KF
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 14:04:14 +0000
+Received: from buildd by hasse.debian.org with local (Exim 4.77)
+ (envelope-from <buildd at hasse.debian.org>)
+ id 1S8XlN-0000ff-L1; Fri, 16 Mar 2012 14:04:13 +0000
+From: buildd on hasse <buildd at hasse.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hasse.debian.org
+Subject: Log for successful build of bedtools_2.16.1-1 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Rksgk-0000DM-St at hummel.debian.org>
-Date: Wed, 11 Jan 2012 07:33:38 +0000
+Message-Id: <E1S8XlN-0000ff-L1 at hasse.debian.org>
+Date: Fri, 16 Mar 2012 14:04:13 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hummel.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hasse.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (armhf) 11 Jan 2012 07:09 ║
+║ bedtools 2.16.1-1 (armhf) 16 Mar 2012 13:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: armhf
-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]
+Get:1 http://incoming.debian.org unstable InRelease [198 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [198 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6213 kB]
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 [6000 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6213 kB]
Get:6 http://ftp.uk.debian.org unstable/contrib Sources [54.4 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [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]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.8 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [5650 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [35.6 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [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]
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2223 B]
+Get:11 http://ftp.uk.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:12 http://ftp.uk.debian.org unstable/main Translation-en [3902 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main armhf Packages [5650 kB]
+Get:16 http://incoming.debian.org unstable/contrib armhf Packages [35.6 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [61.5 kB]
+Get:22 http://incoming.debian.org Packages [696 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.1 MB in 1min 16s (367 kB/s)
+Fetched 33.1 MB in 1min 19s (416 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 3s (285 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,14 +122,14 @@ Checking correctness of dependencies...
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 (2.13-24)
+libc6-dev: already installed (2.13-27)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1+b1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -155,60 +157,62 @@ The following NEW packages will be installed:
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.
+0 upgraded, 32 newly installed, 0 to remove and 4 not upgraded.
+Need to get 16.4 MB of archives.
+After this operation, 42.0 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main libncursesw5 armhf 5.9-4+b1 [293 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.0-5+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:2 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libssl1.0.0 armhf 1.0.0h-1 [962 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.10-1 [246 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 8.12-4+b1 [222 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.30.2-6 [1673 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.7.8.dfsg-7 [779 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.4-2 [134 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libexpat1 armhf 2.0.1-7.2+b1 [106 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libdb4.8 armhf 4.8.30-11 [590 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.1 [203 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-6+b1 [1027 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.1-1 [1009 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.10-1 [52.4 kB]
Get:17 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-5+b1 [132 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armhf 3.7.9-2+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:18 http://ftp.uk.debian.org/debian/ unstable/main libsqlite3-0 armhf 3.7.10-1 [371 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main python2.7-minimal armhf 2.7.3~rc1-1 [1595 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main python2.7 armhf 2.7.3~rc1-1 [2635 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
Get:25 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
Get:26 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-5+b1 [1920 kB]
Get:27 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:28 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
Get:30 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-2 [27.4 kB]
-Get:31 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.50-2 [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]
+Get:31 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:32 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.6.dfsg-2 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 16.1 MB in 2s (6458 kB/s)
+Fetched 16.4 MB in 4s (3526 kB/s)
Selecting previously unselected package libncursesw5.
-(Reading database ... 10684 files and directories currently installed.)
+(Reading database ... 12757 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_armhf.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_armhf.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_armhf.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_armhf.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_armhf.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_armhf.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_armhf.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_armhf.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_armhf.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_armhf.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_armhf.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_armhf.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_armhf.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2+b1_armhf.deb) ...
Selecting previously unselected package libunistring0.
@@ -216,31 +220,29 @@ 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+b1_armhf.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ...
Selecting previously unselected package groff-base.
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+b1_armhf.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_armhf.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_armhf.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2+b1_armhf.deb) ...
+Unpacking file (from .../archives/file_5.10-1_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_armhf.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2+b1_armhf.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_armhf.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_armhf.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_armhf.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_armhf.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_armhf.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
Selecting previously unselected package gettext.
@@ -250,59 +252,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_armhf.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armhf.deb) ...
Setting up libncursesw5 (5.9-4+b1) ...
-Setting up libpipeline1 (1.2.0-5+b1) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4+b1) ...
Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-4+b1) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2+b1) ...
Setting up libunistring0 (0.9.3-5+b1) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3+b1) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.0.2-3+b1) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2+b1) ...
-Setting up file (5.09-2+b1) ...
+Setting up file (5.10-1) ...
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) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15+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+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
-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
+Kernel: Linux 3.2.0-2-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.9-1
+Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2012.01.08 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-15 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-3 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libalgorithm-diff-perl_1.19.02-2 libalgorithm-merge-perl_0.08-2 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2+b1 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-4 libmpc2_0.9-4+b1 libmpfr4_3.1.0-4 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.9-1 login_1:4.1.5-1 lsb-base_3.2+Debian31 make_3.81-8.1+b1 man-db_2.6.1-1 manpages_3.35-0.1 manpages-dev_3.35-0.1 mawk_1.3.3-16+b1 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -313,12 +315,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -329,24 +331,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -359,52 +375,44 @@ 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_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -444,143 +452,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -589,59 +592,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -649,6 +650,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -656,84 +663,156 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-armhf-CNb06x/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-armhf-cuD_vP/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedtools contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org> >../bedtools_2.15.0-1_armhf.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org> >../bedtools_2.16.1-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0733
+Build finished at 20120316-1404
-bedtools_2.15.0-1_armhf.changes:
+bedtools_2.16.1-1_armhf.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: armhf
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org>
+Maintainer: armhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- c7c8799c8d9a457b5588b51a3dd9bc5e90937b1b 349698 bedtools_2.15.0-1_armhf.deb
+ 09871415f8afe7fef890051540cec22ff76c99a6 383636 bedtools_2.16.1-1_armhf.deb
Checksums-Sha256:
- 74283e6a92accd13bd7127ababb8e10a5641c8783a1021ed680479810e1d02e2 349698 bedtools_2.15.0-1_armhf.deb
+ f20bb01e537268a79e5789862157e61ed7f59845a6657db886f750778f4fb553 383636 bedtools_2.16.1-1_armhf.deb
Files:
- 56e0c970edd89cd763a8bed32fdc6782 349698 science optional bedtools_2.15.0-1_armhf.deb
+ 66425f372ea8459df6508fec03eaa213 383636 science optional bedtools_2.16.1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_armhf.deb
+bedtools_2.16.1-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 349698 bytes: control archive= 1866 bytes.
+ size 383636 bytes: control archive= 1972 bytes.
864 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 871
+ Installed-Size: 958
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -749,54 +828,58 @@ bedtools_2.15.0-1_armhf.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 919800 2012-03-16 14:03 ./usr/bin/bedtools
+-rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/linksBed
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/nucBed
+-rwxr-xr-x root/root 36 2012-03-16 14:03 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/tagBam
+-rwxr-xr-x root/root 29 2012-03-16 14:03 ./usr/bin/sortBed
+-rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/mapBed
+-rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/expandCols
+-rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 36 2012-03-16 14:03 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/closestBed
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-03-16 14:03 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 34 2012-03-16 14:03 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 28 2012-03-16 14:03 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 29 2012-03-16 14:03 ./usr/bin/slopBed
+-rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 30 2012-03-16 14:03 ./usr/bin/flankBed
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 31 2012-03-16 14:03 ./usr/bin/randomBed
+-rwxr-xr-x root/root 33 2012-03-16 14:03 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-03-16 14:03 ./usr/bin/complementBed
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 13:39 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 14:03 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -810,7 +893,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-93040c22-317b-4469-a310-c75a2deb431f/build/buildd-bedtools_2.15.0-1-armhf-CNb06x
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-55323db0-9268-44ad-b050-6eb0a35707d6/build/buildd-bedtools_2.16.1-1-armhf-cuD_vP
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -818,18 +901,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 66004
-Build-Time: 1195
+Build-Space: 75200
+Build-Time: 1464
Distribution: sid
-Install-Time: 128
-Job: bedtools_2.15.0-1
+Install-Time: 92
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 1428
-Source-Version: 2.15.0-1
-Space: 66004
+Package-Time: 1668
+Source-Version: 2.16.1-1
+Space: 75200
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0733
-Build needed 00:23:48, 66004k disc space
+Finished at 20120316-1404
+Build needed 00:27:48, 75200k disc space
+Signature with key '0B213A80' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 5efdc49..71ab708 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,68 +1,60 @@
-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])
+From buildd at mozart.debian.net Fri Mar 16 12:33:55 2012
+Return-path: <buildd at mozart.debian.net>
+Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (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)
+ (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
+ id 1S8WLy-0005l6-4d
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:33:55 +0000
+Received: from mozart.debian.net ([10.1.0.1])
+ by callisto.debian.net with esmtp (Exim 4.72)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1S8WLt-00086O-Nq; Fri, 16 Mar 2012 12:33:49 +0000
+Received: from buildd by mozart.debian.net with local (Exim 4.76)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1S8WM1-0002kj-KW; Fri, 16 Mar 2012 12:33:57 +0000
+From: Build Daemon <buildd at mozart.debian.net>
+To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
+ logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.16.1-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RksXu-0006VQ-CG at ironforge.sceen.net>
-Date: Wed, 11 Jan 2012 08:24:30 +0100
+Message-Id: <E1S8WM1-0002kj-KW at mozart.debian.net>
+Date: Fri, 16 Mar 2012 12:33:57 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (hurd-i386) 11 Jan 2012 08:18 ║
+║ bedtools 2.16.1-1 (hurd-i386) 16 mars 2012 12:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: hurd-i386
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.fr.debian.org sid/main Sources/DiffIndex
+Ign http://ftp.debian-ports.org unreleased InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
Hit http://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 ftp://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Get:2 ftp://ftp.debian-ports.org unreleased/main TranslationIndex
-Ign http://incoming.debian.org sid/contrib Translation-en
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Get:2 http://incoming.debian.org Release [1616 B]
+Hit http://ftp.fr.debian.org sid/contrib Translation-en
+Hit http://ftp.fr.debian.org sid/main Translation-en
+Get:3 http://incoming.debian.org Sources [58.9 kB]
+Hit http://ftp.debian-ports.org unreleased Release
+Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:4 http://incoming.debian.org Packages [687 kB]
+Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
Ign http://incoming.debian.org Translation-en
-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
+Fetched 748 kB in 1min 2s (12.0 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +75,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 4s (198 kB/s)
Download complete and in download only mode
Check arch
@@ -108,19 +100,19 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- groff-base libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
- man-db
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -137,142 +129,105 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42-1)
+e2fsprogs: already installed (1.42.1-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-2)
+gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-hurd: already installed (20111106-1)
+hurd: already installed (20111206-1)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
sysvinit-utils: already installed (2.88dsf-13.13)
sysvinit: already installed (2.88dsf-13.13)
-tar: already installed (1.26-3)
+tar: already installed (1.26-2)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
-libc0.3-dev: already installed (2.13-24)
+libc0.3-dev: already installed (2.13-25)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
-hurd-dev: already installed (20111106-1)
+hurd-dev: already installed (20111206-1)
cdbs: missing
-debhelper: missing
-Using default version 8.9.14
+debhelper: already installed (9.20120115 >= 8 is satisfied)
quilt: missing
python: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: already installed (1:1.2.6.dfsg-1)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt python
+Installing positive dependencies: cdbs quilt python
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libdb4.8 libexpat1 libmagic1 libsqlite3-0 libunistring0 mime-support
- po-debconf python-minimal python2.7 python2.7-minimal
+ diffstat libdb4.8 libsqlite3-0 mime-support python-minimal python2.7
+ python2.7-minimal
Suggested packages:
- devscripts dh-make gettext-doc libmail-box-perl python-doc python-tk
- python2.7-doc binfmt-support procmail graphviz default-mta
- mail-transport-agent
+ devscripts 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 libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text 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, 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.
+ cdbs diffstat libdb4.8 libsqlite3-0 mime-support python python-minimal
+ python2.7 python2.7-minimal quilt
+0 upgraded, 10 newly installed, 0 to remove and 89 not upgraded.
+Need to get 0 B/6107 kB of archives.
+After this operation, 18.6 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- 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
+ libdb4.8 libsqlite3-0 mime-support python2.7-minimal python2.7
+ python-minimal python cdbs diffstat quilt
Authentication warning overridden.
-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.
+(Reading database ... 15865 files and directories currently installed.)
Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_hurd-i386.deb) ...
-Selecting previously unselected package 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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_hurd-i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_hurd-i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_hurd-i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_hurd-i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.2-11_hurd-i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
-Selecting previously unselected package gettext.
-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+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_hurd-i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Processing triggers for man-db ...
-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 libsqlite3-0 (3.7.9-3) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
-Setting up 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+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up python2.7-minimal (2.7.2-11) ...
+Setting up python2.7 (2.7.2-11) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
+Setting up quilt (0.60-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-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
+Toolchain package versions: binutils_2.22-5+hurd.1 dpkg-dev_1.16.1.1 g++-4.5_4.5.3-9 g++-4.6_4.6.2-16+hurd.1 gcc-4.4_4.4.6-14 gcc-4.5_4.5.3-9 gcc-4.6_4.6.2-16+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20111206-1 libc0.3-dev_2.13-25 libstdc++6_4.6.2-16+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.2-16+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.22-5+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.4_4.4.6-14 cpp-4.5_4.5.3-9 cpp-4.6_4.6.2-16+hurd.1 cron_3.0pl1-120 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120115 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2012.01.08 debianutils_4.0.4 deborphan_1.7.28.5 dialog_1.1-20111020-1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.1-1+hurd.1 file_5.10-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3.1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.2-16+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.2-4 gcc-4.4_4.4.6-14 gcc-4.4-base_4.4.6-14 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-16+hurd.1 gcc-4.6-base_4.6.2-16+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.6_4.6.2-16+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-14 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20111206-1 hurd-dev_20111206-1 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libapt-pkg-dev_0.8.15.9 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libboost-iostreams1.46.1_1.46.1-8 libboost-iostreams1.48.0_1.48.0-3 libbz2-1.0_1.0.6-1 libc-bin_2.13-25 libc-dev-bin_2.13-25 libc0.3_2.13-25 libc0.3-dev_2.13-25 libc0.3-xen_2.13-25 libclass-isa-perl_0.36-2 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libcwidget3_0.5.16-3.1 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.1 libelfg0_0.8.13-3 libept-dev_1.0.5 libept1_1.0.5 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libfontconfig1_2.8.0-3.1 libfreetype6_2.4.8-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-16+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.2-16+hurd.1 libglib2.0-0_2.30.2-6 libglib2.0-data_2.28.8-1 libgmp10_2:5.0.4+dfsg-1 libgnutls26_2.12.17-2 libgomp1_4.6.2-16+hurd.1 libgpg-error0_1.10-3 libldap-2.4-2_2.4.28-1.1 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libobjc2_4.5.3-9 libp11-kit0_0.12-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-7 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.47-1 libpopt0_1.16-3 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.2-16+hurd.1 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-4 libsasl2-modules_2.1.25.dfsg1-4 libsigc++-2.0-0c2a_2.2.9-1.1 libsigsegv2_2.9-4 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-16+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.2-16+hurd.1 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.13-1 libtasn1-3_2.11-1 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.20.1-4 libwibble-dev_0.1.26-1 libxapian-dev_1.2.7-1 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-7 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mime-support_3.52-1 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.16-1+hurd.1 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011n-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-1 zlib1g-dev_1:1.2.6.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,12 +238,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -299,24 +254,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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_2.15.0-1-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -329,52 +298,44 @@ 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_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -414,204 +375,197 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
+ * compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
+ * compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
- * compiling genomeFile.cpp
-
- Building in src/annotateBed
+ * compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
- * compiling annotateMain.cpp
* compiling annotateBed.cpp
-
- Building in src/bamToBed
+ * compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
- * compiling bamToBed.cpp
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
+ * compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * compiling bedToBam.cpp
-
- Building in src/bedpeToBam
+ * compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
- * compiling bedpeToBam.cpp
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
+ * compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
- * compiling clusterMain.cpp
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
+ * compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
- * 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
-
+groupBy.cpp: In function 'int groupby_main(int, char**)':
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
+ * compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
- * compiling mergeMain.cpp
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
- * compiling multiBamCovMain.cpp
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
+ * compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- * compiling pairToBedMain.cpp
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
-
- Building in src/pairToPair
+ * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
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]
- * compiling pairToPairMain.cpp
* compiling pairToPair.cpp
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
+ * compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling subtractMain.cpp
* compiling subtractBed.cpp
-
- Building in src/tagBam
+ * compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling tagBamMain.cpp
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
+ * compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * compiling unionBedGraphsMain.cpp
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -619,6 +573,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -626,83 +586,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
- dpkg-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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.16.1-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0824
+Build finished at 20120316-1232
-bedtools_2.15.0-1_hurd-i386.changes:
+bedtools_2.16.1-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- fa1d072696e136583ce07dafe49ebf0a8947e583 402344 bedtools_2.15.0-1_hurd-i386.deb
+ ebc62c6fbc856685c98460882a23493fcf1d8267 443564 bedtools_2.16.1-1_hurd-i386.deb
Checksums-Sha256:
- 5c9ab8161f838bb6ddd8b5386c60a04551aeadc70d3e9303010a7458e423dac3 402344 bedtools_2.15.0-1_hurd-i386.deb
+ e1f4ed7099dc003fe3dcf6f58de97f708e677657f9f213b467a79e4f37f56e5a 443564 bedtools_2.16.1-1_hurd-i386.deb
Files:
- 240b0a7f1d5999b7ebd90b8328b5feac 402344 science optional bedtools_2.15.0-1_hurd-i386.deb
+ 34f11720cbc1244c01aac14d545c7152 443564 science optional bedtools_2.16.1-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_hurd-i386.deb
+bedtools_2.16.1-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 402344 bytes: control archive= 1868 bytes.
+ size 443564 bytes: control archive= 1984 bytes.
869 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1279
+ Installed-Size: 1430
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -718,54 +750,58 @@ bedtools_2.15.0-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:31 ./
+drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:32 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 12:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:19 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 12:32 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 12:30 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1403068 2012-03-16 12:32 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/mapBed
+-rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:30 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:30 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 12:30 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-03-16 12:30 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-03-16 12:30 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:30 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 12:30 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-03-16 12:30 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-03-16 12:30 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 12:30 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -779,55 +815,39 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.15.0-1-hurd-i386-uDqAvh
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.16.1-1-hurd-i386-h7dKNv
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 89 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libcwidget3 libsigc++-2.0-0c2a adduser libboost-iostreams1.46.1
+ libcwidget3 libsigc++-2.0-0c2a libboost-iostreams1.46.1
+ libboost-iostreams1.48.0 libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- 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.)
+ cdbs* diffstat* libdb4.8* libsqlite3-0* mime-support* python*
+ python-minimal* python2.7* python2.7-minimal* quilt*
+0 upgraded, 0 newly installed, 10 to remove and 89 not upgraded.
+After this operation, 18.6 MB disk space will be freed.
+(Reading database ... 16834 files and directories currently installed.)
Removing cdbs ...
-Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
Removing python ...
Purging configuration files for python ...
Removing python2.7 ...
Purging configuration files for python2.7 ...
Removing libdb4.8 ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
Removing libsqlite3-0 ...
Purging configuration files for libsqlite3-0 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
Removing mime-support ...
Purging configuration files for mime-support ...
Removing python-minimal ...
@@ -840,18 +860,18 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 62160
-Build-Time: 234
+Build-Space: 71620
+Build-Time: 788
Distribution: sid
-Install-Time: 42
-Job: bedtools_2.15.0-1
+Install-Time: 114
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 358
-Source-Version: 2.15.0-1
-Space: 62160
+Package-Time: 1049
+Source-Version: 2.16.1-1
+Space: 71620
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0824
-Build needed 00:05:58, 62160k disc space
+Finished at 20120316-1232
+Build needed 00:17:29, 71620k disc space
diff --git a/i386.log b/i386.log
index db2a33f..5af347d 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,70 @@
-From buildd at biber.debian.org Wed Jan 11 07:19:45 2012
+From buildd at biber.debian.org Fri Mar 16 12:53:00 2012
Return-path: <buildd at biber.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+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 biber.debian.org>)
- id 1RksTJ-0008EB-Dl
- for logs at buildd.debian.org; Wed, 11 Jan 2012 07:19:45 +0000
+ id 1S8WeR-0002Hx-QQ
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:52:59 +0000
Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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)
+ by kokkonen.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
+ id 1S8WeQ-0007vd-OL; Fri, 16 Mar 2012 12:52:58 +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>
+ id 1S8WeP-0005SP-R3; Fri, 16 Mar 2012 12:52:57 +0000
+Message-Id: <E1S8WeP-0005SP-R3 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: Wed, 11 Jan 2012 07:19:43 +0000
+Date: Fri, 16 Mar 2012 12:52:57 +0000
From: buildd on biber <buildd at biber.debian.org>
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on i386 (dist=sid)
-Key-Id: C83D412C
+Subject: Log for successful build of bedtools_2.16.1-1 on i386 (dist=sid)
+Key-Id: 6EBCB100
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (i386) 11 Jan 2012 07:15 ║
+║ bedtools 2.16.1-1 (i386) 16 Mar 2012 12:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [189 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [6000 kB]
+Get:1 http://ftp.gr.debian.org unstable InRelease [198 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [6213 kB]
Get:3 http://ftp.gr.debian.org unstable/contrib Sources [54.4 kB]
-Get:4 http://ftp.gr.debian.org unstable/non-free Sources [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]
+Get:4 http://ftp.gr.debian.org unstable/non-free Sources [99.8 kB]
+Get:5 http://ftp.gr.debian.org unstable/main i386 Packages [5912 kB]
+Get:6 http://incoming.debian.org unstable InRelease [198 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [45.6 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2085 B]
-Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2223 B]
+Get:9 http://ftp.gr.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:10 http://ftp.gr.debian.org unstable/main Translation-en [3902 kB]
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 [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]
+Get:11 http://incoming.debian.org Release.gpg [836 B]
+Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main i386 Packages [5912 kB]
+Get:16 http://incoming.debian.org unstable/contrib i386 Packages [45.6 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [60.2 kB]
+Get:22 http://incoming.debian.org Packages [696 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 29.4 MB in 13s (2138 kB/s)
+Fetched 33.7 MB in 21s (1542 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +85,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 3s (312 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +109,12 @@ 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 11 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 11 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,38 +123,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
+base-files: already installed (6.7)
base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
-diffutils: already installed (1:3.2-1)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.2.1)
+diffutils: already installed (1:3.2-2)
dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+e2fsprogs: already installed (1.42.1-2)
findutils: already installed (4.4.2-4)
grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.09)
+hostname: already installed (3.11)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+login: already installed (1:4.1.5-1)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
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)
+bsdutils: already installed (1:2.20.1-4)
+mount: already installed (2.20.1-4)
+util-linux: already installed (2.20.1-4)
+libc6-dev: already installed (2.13-27)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -180,60 +182,62 @@ The following NEW packages will be installed:
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.
+0 upgraded, 32 newly installed, 0 to remove and 11 not upgraded.
+Need to get 19.3 MB of archives.
+After this operation, 52.7 MB of additional disk space will be used.
Get:1 http://ftp.gr.debian.org/debian/ unstable/main libncursesw5 i386 5.9-4 [330 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-5 [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:2 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.1-1 [38.6 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main libssl1.0.0 i386 1.0.0h-1 [2862 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.10-1 [249 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.30.2-6 [1823 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-7 [885 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.4-2 [151 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libexpat1 i386 2.0.1-7.2 [137 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libdb4.8 i386 4.8.30-11 [729 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.1 [205 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.1-1 [1052 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.10-1 [52.4 kB]
Get:17 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-5 [133 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main libsqlite3-0 i386 3.7.9-2 [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:18 http://ftp.gr.debian.org/debian/ unstable/main libsqlite3-0 i386 3.7.10-1 [442 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main python2.7-minimal i386 2.7.3~rc1-1 [1719 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main python2.7 i386 2.7.3~rc1-1 [2693 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:23 http://ftp.gr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:24 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
Get:25 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
Get:26 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-5 [2025 kB]
Get:27 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:28 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:29 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.14 [693 kB]
+Get:29 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
Get:30 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-2 [29.3 kB]
-Get:31 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.50-2 [381 kB]
-Get:32 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+Get:31 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:32 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.6.dfsg-2 [210 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 19.1 MB in 1s (15.6 MB/s)
+Fetched 19.3 MB in 1s (10.6 MB/s)
Selecting previously unselected package libncursesw5.
-(Reading database ... 10722 files and directories currently installed.)
+(Reading database ... 10798 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_i386.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_i386.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_i386.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_i386.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_i386.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_i386.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_i386.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_i386.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_i386.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_i386.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_i386.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_i386.deb) ...
Selecting previously unselected package libunistring0.
@@ -241,31 +245,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_i386.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_i386.deb) ...
+Unpacking file (from .../archives/file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously unselected package gettext.
@@ -275,59 +277,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_i386.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
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 11 not upgraded.
Checking correctness of dependencies...
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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.7-1
+Package versions: apt_0.8.15.9 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.12-3 gpgv_1.4.12-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libquadmath0_4.6.3-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.7-1 login_1:4.1.5-1 lsb-base_3.2+Debian29 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -338,12 +340,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -354,24 +356,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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-i386-1HqqaM/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -384,52 +400,44 @@ 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_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -469,143 +477,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -614,59 +617,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -674,6 +675,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -681,46 +688,118 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-i386-1HqqaM/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-i386-Y60OvV/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.15.0-1_i386.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.16.1-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0719
+Build finished at 20120316-1252
-bedtools_2.15.0-1_i386.changes:
+bedtools_2.16.1-1_i386.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -728,36 +807,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- c1cbde2217a5dd1ff2d8956e2b06429100909a16 402140 bedtools_2.15.0-1_i386.deb
+ 6fecdcee8b252ddf31ee4c589cd9b48dea74d702 443690 bedtools_2.16.1-1_i386.deb
Checksums-Sha256:
- 917d0073e3a7147c70acc0a339329b28e3bedc5266160967374009e3cdcc99a2 402140 bedtools_2.15.0-1_i386.deb
+ 04d15e827e69504a80711494afe9f4cef5e17ecd7fbb5832bfdede08313555c2 443690 bedtools_2.16.1-1_i386.deb
Files:
- 3853cf76f932189e25a03f756dcd5067 402140 science optional bedtools_2.15.0-1_i386.deb
+ 586a70855d6e9d1defb821e8943e02e8 443690 science optional bedtools_2.16.1-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_i386.deb
+bedtools_2.16.1-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 402140 bytes: control archive= 1864 bytes.
+ size 443690 bytes: control archive= 1978 bytes.
864 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1277
+ Installed-Size: 1430
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -773,54 +852,58 @@ bedtools_2.15.0-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 36 2012-03-16 12:52 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/flankBed
+-rwxr-xr-x root/root 29 2012-03-16 12:52 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 1403068 2012-03-16 12:52 ./usr/bin/bedtools
+-rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/windowBed
+-rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 31 2012-03-16 12:52 ./usr/bin/randomBed
+-rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/tagBam
+-rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 30 2012-03-16 12:52 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/mapBed
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/complementBed
+-rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 36 2012-03-16 12:52 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 35 2012-03-16 12:52 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:52 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 34 2012-03-16 12:52 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 32 2012-03-16 12:52 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-03-16 12:52 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 29 2012-03-16 12:52 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2012-03-16 12:52 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:49 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -834,7 +917,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-67c75f87-be53-49e4-82b0-725c3ba5267a/build/buildd-bedtools_2.15.0-1-i386-1HqqaM
+Purging /var/lib/schroot/mount/sid-i386-sbuild-efc38c0f-ecec-4245-8b7f-ce411fa8dba3/build/buildd-bedtools_2.16.1-1-i386-Y60OvV
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -842,18 +925,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 62100
-Build-Time: 169
+Build-Space: 71588
+Build-Time: 201
Distribution: sid
Install-Time: 58
-Job: bedtools_2.15.0-1
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 258
-Source-Version: 2.15.0-1
-Space: 62100
+Package-Time: 298
+Source-Version: 2.16.1-1
+Space: 71588
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0719
-Build needed 00:04:18, 62100k disc space
-Signature with key 'C83D412C' requested:
+Finished at 20120316-1252
+Build needed 00:04:58, 71588k disc space
+Signature with key '6EBCB100' requested:
diff --git a/ia64.log b/ia64.log
index f230f75..d3aeece 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,66 +1,69 @@
-From buildd at mundy.debian.org Wed Jan 11 07:22:42 2012
-Return-path: <buildd at mundy.debian.org>
+From buildd at alkman.debian.org Fri Mar 16 13:26:06 2012
+Return-path: <buildd at alkman.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from 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 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])
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1S8XAU-0008CO-L6
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 13:26:06 +0000
+Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
+ CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at 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)
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1S8XAS-00023V-U3
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 13:26:05 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alkman.debian.org>)
+ id 1S8XAQ-0002sS-Pl; Fri, 16 Mar 2012 13:26:02 +0000
+Date: Fri, 16 Mar 2012 13:26:02 +0000
+Message-Id: <E1S8XAQ-0002sS-Pl at alkman.debian.org>
+From: buildd on alkman <buildd at alkman.debian.org>
+To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.16.1-1 on ia64 (dist=sid)
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 mundy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (ia64) 11 Jan 2012 07:11 ║
+║ bedtools 2.16.1-1 (ia64) 16 Mar 2012 13:11 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: ia64
-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:1 http://spohr.debian.org unstable InRelease [198 kB]
+Get:2 http://incoming.debian.org unstable InRelease [198 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [6213 kB]
Get:4 http://spohr.debian.org unstable/contrib Sources [54.4 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [100 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [7645 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [99.8 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [5659 kB]
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 [6000 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.7 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6213 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [37.4 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2085 B]
-Ign http://spohr.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 ia64 Packages [7645 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.7 kB]
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2223 B]
+Get:11 http://spohr.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:12 http://spohr.debian.org unstable/main Translation-en [3902 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main ia64 Packages [5659 kB]
+Get:16 http://incoming.debian.org unstable/contrib ia64 Packages [37.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [60.0 kB]
+Get:22 http://incoming.debian.org Packages [691 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.7 MB in 18s (1565 kB/s)
+Fetched 33.2 MB in 28s (1170 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,11 +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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (873 kB/s)
Download complete and in download only mode
Check arch
@@ -99,7 +102,7 @@ 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...
@@ -108,7 +111,7 @@ 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 62 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -116,7 +119,7 @@ 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 62 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,37 +129,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, 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 (4.2.1)
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)
+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 (3.06)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-3)
+perl-base: already installed (5.14.2-7)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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)
-libc6.1-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)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6.1-dev: already installed (2.13-26)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 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 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -173,7 +176,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -187,60 +190,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 50 not upgraded.
+Need to get 21.3 MB of archives.
+After this operation, 66.6 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ unstable/main zlib1g ia64 1:1.2.6.dfsg-2 [117 kB]
+Get:2 http://spohr.debian.org/debian/ unstable/main libncursesw5 ia64 5.9-4 [387 kB]
+Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.1-1 [48.2 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main libssl1.0.0 ia64 1.0.0h-1 [1565 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.10-1 [274 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main libffi5 ia64 3.0.10-3 [35.5 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.30.2-6 [2198 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-7 [1179 kB]
+Get:10 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.4-2 [174 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libexpat1 ia64 2.0.1-7.2 [212 kB]
+Get:12 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
+Get:13 http://spohr.debian.org/debian/ unstable/main libdb4.8 ia64 4.8.30-11 [1117 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 9.0.1 [240 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.1-1 [1156 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main file ia64 5.10-1 [55.2 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
+Get:19 http://spohr.debian.org/debian/ unstable/main libsqlite3-0 ia64 3.7.10-1 [639 kB]
+Get:20 http://spohr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://spohr.debian.org/debian/ unstable/main python2.7-minimal ia64 2.7.3~rc1-1 [2192 kB]
+Get:22 http://spohr.debian.org/debian/ unstable/main python2.7 ia64 2.7.3~rc1-1 [2892 kB]
+Get:23 http://spohr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://spohr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
+Get:27 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 kB]
+Get:28 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://spohr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.55-2 [37.2 kB]
+Get:32 http://spohr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.6.dfsg-2 [251 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 20.8 MB in 19s (1042 kB/s)
+Fetched 21.3 MB in 8s (2576 kB/s)
+(Reading database ... 10668 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_ia64.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10648 files and directories currently installed.)
+(Reading database ... 10668 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_ia64.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_ia64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_ia64.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_ia64.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_ia64.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_ia64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_ia64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_ia64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_ia64.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_ia64.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_ia64.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_ia64.deb) ...
Selecting previously unselected package libunistring0.
@@ -248,31 +260,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_ia64.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_ia64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_ia64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_ia64.deb) ...
+Unpacking file (from .../archives/file_5.10-1_ia64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_ia64.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_ia64.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_ia64.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-9_ia64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_ia64.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-9_ia64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_ia64.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously unselected package gettext.
@@ -282,50 +292,50 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_ia64.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_ia64.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-9) ...
-Setting up python2.7 (2.7.2-9) ...
-Setting up python-minimal (2.7.2-9) ...
-Setting up python (2.7.2-9) ...
-Setting up cdbs (0.4.100) ...
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -333,11 +343,11 @@ 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 62 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6.1-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.2-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6.1_2.13-26 libc6.1-dev_2.13-26 libclass-isa-perl_0.36-3 libcloog-ppl0_0.15.11-4 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgmpxx4ldbl_2:5.0.3+dfsg-1 libgomp1_4.6.2-12 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libppl-c4_0.11.2-6 libppl9_0.11.2-6 libpwl5_0.11.2-6 libquadmath0_4.6.2-12 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.2-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -348,12 +358,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -364,24 +374,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" 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_2.15.0-1-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="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -394,52 +418,44 @@ 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_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -478,148 +494,143 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -628,59 +639,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -688,6 +697,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -695,83 +710,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-ia64-bPioEU/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-ia64-8FJa2_/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.15.0-1_ia64.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.16.1-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0722
+Build finished at 20120316-1325
-bedtools_2.15.0-1_ia64.changes:
+bedtools_2.16.1-1_ia64.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
+Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 13ffad7622df6d784dfd1f7114be353c6439f8db 500864 bedtools_2.15.0-1_ia64.deb
+ 5fe4f50408eb6aecaca594ed2df7c32e364b66d5 554952 bedtools_2.16.1-1_ia64.deb
Checksums-Sha256:
- 0010e3bac861b4c0bf31986e6f9887ddd4085670522a0d6aa066174578434a66 500864 bedtools_2.15.0-1_ia64.deb
+ b7c2679048e1719d8f4e56902ea5d493d90ee47823566d41531b6e6cc376b3e5 554952 bedtools_2.16.1-1_ia64.deb
Files:
- 4968cb15350537dc0c7cbbcad2f51458 500864 science optional bedtools_2.15.0-1_ia64.deb
+ 54491056fab0589c0e567a0aed56235f 554952 science optional bedtools_2.16.1-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_ia64.deb
+bedtools_2.16.1-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 500864 bytes: control archive= 1875 bytes.
+ size 554952 bytes: control archive= 1984 bytes.
878 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 2616
+ Installed-Size: 2904
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6.1 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -787,54 +874,58 @@ bedtools_2.15.0-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/bin/
+-rwxr-xr-x root/root 2947432 2012-03-16 13:25 ./usr/bin/bedtools
+-rwxr-xr-x root/root 36 2012-03-16 13:25 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/windowBed
+-rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/tagBam
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-03-16 13:25 ./usr/bin/sortBed
+-rwxr-xr-x root/root 29 2012-03-16 13:25 ./usr/bin/slopBed
+-rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/randomBed
+-rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/nucBed
+-rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/mapBed
+-rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 13:25 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-03-16 13:25 ./usr/bin/flankBed
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 31 2012-03-16 13:25 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/complementBed
+-rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 32 2012-03-16 13:25 ./usr/bin/closestBed
+-rwxr-xr-x root/root 28 2012-03-16 13:25 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 36 2012-03-16 13:25 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 13:25 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 33 2012-03-16 13:25 ./usr/bin/annotateBed
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 13:14 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 13:25 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -848,7 +939,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-3830c53a-73f0-493d-af9d-3152f21444bb/build/buildd-bedtools_2.15.0-1-ia64-bPioEU
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-63cdf3bb-1ec5-4067-923f-5e97de6f9b23/build/buildd-bedtools_2.16.1-1-ia64-8FJa2_
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -856,19 +947,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 111456
-Build-Time: 516
+Build-Space: 138532
+Build-Time: 681
Distribution: sid
-Install-Time: 113
-Job: bedtools_2.15.0-1
+Install-Time: 111
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 683
-Source-Version: 2.15.0-1
-Space: 111456
+Package-Time: 856
+Source-Version: 2.16.1-1
+Space: 138532
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0722
-Build needed 00:11:23, 111456k disc space
-Signature with key '66C872EA' requested:
+Finished at 20120316-1325
+Build needed 00:14:16, 138532k disc space
+Signature with key '94AE7BC0' requested:
diff --git a/info b/info
index a3475de..716bd80 100644
--- a/info
+++ b/info
@@ -1,13 +1,13 @@
-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
+s390x~1331900322~sid~successful
+kfreebsd-i386~1331900511~sid~successful
+s390~1331900808~sid~successful
+hurd-i386~1331901235~sid~successful
+mipsel~1331901700~sid~successful
+i386~1331902380~sid~successful
+armel~1331902487~sid~successful
+mips~1331902619~sid~successful
+ia64~1331904367~sid~successful
+sparc~1331905264~sid~successful
+armhf~1331906656~sid~successful
+powerpc~1331907608~sid~successful
+kfreebsd-amd64~1331917049~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 5661425..550984e 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,49 +1,62 @@
-From buildd at fano.debian.org Wed Jan 11 07:27:40 2012
-Return-path: <buildd at fano.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at fasch.debian.org Fri Mar 16 16:57:26 2012
+Return-path: <buildd at fasch.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from 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 fano.debian.org>)
- 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])
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1S8aSz-0004xK-St
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 16:57:26 +0000
+Received: from fasch.debian.org ([194.177.211.201])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 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 1Rksau-0000ZP-Cu; Wed, 11 Jan 2012 07:27:36 +0000
-Message-Id: <E1Rksau-0000ZP-Cu at fano.debian.org>
+ CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1S8aSx-0001Ma-Q2; Fri, 16 Mar 2012 16:57:24 +0000
+Received: from buildd by fasch.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fasch.debian.org>)
+ id 1S8aSw-0001pb-RJ; Fri, 16 Mar 2012 16:57:22 +0000
+Message-Id: <E1S8aSw-0001pb-RJ at fasch.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 11 Jan 2012 07:27:36 +0000
-From: buildd on fano <buildd at fano.debian.org>
+Date: Fri, 16 Mar 2012 16:57:22 +0000
+From: buildd on fasch <buildd at fasch.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.16.1-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: D33FE1D8
+Key-Id: 94C0145B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (kfreebsd-amd64) 11 Jan 2012 07:14 ║
+║ bedtools 2.16.1-1 (kfreebsd-amd64) 16 Mar 2012 16:49 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: kfreebsd-amd64
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 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-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Hit http://incoming.debian.org Release.gpg
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
+Hit http://ftp.gr.debian.org sid/contrib Translation-en
+Hit http://ftp.gr.debian.org sid/main Translation-en
+Hit http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://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
@@ -52,26 +65,14 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Get:2 http://incoming.debian.org Release [1616 B]
+Hit http://incoming.debian.org Release
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
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-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
+Hit http://incoming.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Translation-en
+Hit http://incoming.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org Translation-en
-Fetched 654 kB in 3s (167 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -92,11 +93,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://ftp.gr.debian.org/debian/ sid/main bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 0s (6627 kB/s)
Download complete and in download only mode
Check arch
@@ -116,12 +117,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,38 +131,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
+base-files: already installed (6.7)
base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
-diffutils: already installed (1:3.2-1)
+coreutils: already installed (8.13-3.1)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.2.1)
+diffutils: already installed (1:3.2-2)
dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
-findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds3-2)
+e2fsprogs: already installed (1.42.1-2)
+findutils: already installed (4.4.2-4)
+freebsd-utils: already installed (9.0-2)
grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.09)
+gzip: already installed (1.4-3)
+hostname: already installed (3.11)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+login: already installed (1:4.1.5-1)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
+bsdutils: already installed (1:2.20.1-4)
+util-linux: already installed (2.20.1-4)
libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -171,8 +172,8 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ 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:
@@ -183,53 +184,56 @@ 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 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
+ 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, 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.
+0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/16.7 MB of archives.
+After this operation, 45.2 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 11850 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-amd64.deb) ...
+(Reading database ... 11499 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_kfreebsd-amd64.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_kfreebsd-amd64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_kfreebsd-amd64.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-amd64.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package libdb4.8.
Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-amd64.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
-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) ...
+Unpacking man-db (from .../man-db_2.6.1-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_kfreebsd-amd64.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_kfreebsd-amd64.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_kfreebsd-amd64.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.2-11_kfreebsd-amd64.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext.
@@ -239,52 +243,53 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_kfreebsd-amd64.deb) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.2-11) ...
+Setting up python2.7 (2.7.2-11) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-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
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 kfreebsd-kernel-headers_0.77 libc0.1-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1
+Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 freebsd-utils_9.0-2 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.10-1 groff-base_1.21-6 gzip_1.4-3 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0-2 kfreebsd-kernel-headers_0.77 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbsd0_0.3.0-2 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc0.1_2.13-27 libc0.1-dev_2.13-27 libcam6_9.0+ds1-1 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libgeom1_9.0+ds1-1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 libgssglue1_0.3-4 libjail1_9.0+ds1-1 libkiconv4_9.0+ds1-1 libkvm0_9.0+ds1-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libpng12-0_1.2.47-1 libprocps0_1:3.3.2-3 libquadmath0_4.6.3-1 libreadline6_6.2-8 libsbuf6_9.0+ds1-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 login_1:4.1.5-1 lsb-base_3.2+Debian31 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 procps_1:3.3.2-3 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 type-handling_0.2.23 tzdata_2012b-1 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -295,12 +300,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -311,24 +316,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -341,52 +360,44 @@ 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_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -425,148 +436,143 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -575,59 +581,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -635,6 +639,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -642,83 +652,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../bedtools_2.16.1-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0724
+Build finished at 20120316-1656
-bedtools_2.15.0-1_kfreebsd-amd64.changes:
+bedtools_2.16.1-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- aec4a53f8605e224da0099dfc63c5760f0948511 394590 bedtools_2.15.0-1_kfreebsd-amd64.deb
+ d966edbb0e68c00d12945145593d9e9341b33e25 434400 bedtools_2.16.1-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 1aac10e7ccacbc8ac69d38ef06af1f6d8aed39f3ed3ed1eb720ca31bdc11dc46 394590 bedtools_2.15.0-1_kfreebsd-amd64.deb
+ 9939dca6f2b649229d993e6fae23ed47179f1f0ad4eb86da6bd3f9379ccf3d36 434400 bedtools_2.16.1-1_kfreebsd-amd64.deb
Files:
- 56b50754fd92e7ecaa50d84ad86e3dce 394590 science optional bedtools_2.15.0-1_kfreebsd-amd64.deb
+ 1afb73612304e7654b53fbf558eea4c4 434400 science optional bedtools_2.16.1-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_kfreebsd-amd64.deb
+bedtools_2.16.1-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 394590 bytes: control archive= 1874 bytes.
+ size 434400 bytes: control archive= 1983 bytes.
876 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1241
+ Installed-Size: 1385
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -734,54 +816,58 @@ bedtools_2.15.0-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 16:52 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 16:55 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 16:55 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1388184 2012-03-16 16:55 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/mapBed
+-rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 16:55 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-03-16 16:55 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 16:55 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-03-16 16:55 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-03-16 16:55 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 16:55 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 16:55 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-03-16 16:55 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-03-16 16:55 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 16:55 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -795,23 +881,23 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1326266062-99271/build/buildd-bedtools_2.15.0-1-kfreebsd-amd64-aBYbpV
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1331916571-2471/build/buildd-bedtools_2.16.1-1-kfreebsd-amd64-FwWjjT
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0* libmagic1*
- libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db*
- mime-support* po-debconf* python* python-minimal* python2.7*
+ 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, 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.)
+0 upgraded, 0 newly installed, 28 to remove and 0 not upgraded.
+After this operation, 45.2 MB disk space will be freed.
+(Reading database ... 13771 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -822,6 +908,10 @@ 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 ...
@@ -837,8 +927,6 @@ 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 ...
@@ -861,18 +949,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 101320
-Build-Time: 351
+Build-Space: 118126
+Build-Time: 232
Distribution: sid
-Install-Time: 217
-Job: bedtools_2.15.0-1
+Install-Time: 132
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 593
-Source-Version: 2.15.0-1
-Space: 101320
+Package-Time: 389
+Source-Version: 2.16.1-1
+Space: 118126
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0724
-Build needed 00:09:53, 101320k disc space
-Signature with key 'D33FE1D8' requested:
+Finished at 20120316-1656
+Build needed 00:06:29, 118126k disc space
+Signature with key '94C0145B' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index ae37178..f615341 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,57 +1,57 @@
-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 buildd at finzi.debian.org Fri Mar 16 12:21:51 2012
+Return-path: <buildd at finzi.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 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>
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1S8WAI-0002fV-VJ
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:21:51 +0000
+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 1S8WAH-0005LH-PB; Fri, 16 Mar 2012 12:21:50 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1S8WAF-000KXY-3E; Fri, 16 Mar 2012 12:21:47 +0000
+Message-Id: <E1S8WAF-000KXY-3E at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 11 Jan 2012 07:20:22 +0000
-From: buildd on field <buildd at field.debian.org>
+Date: Fri, 16 Mar 2012 12:21:46 +0000
+From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.16.1-1 on kfreebsd-i386
(dist=sid)
-Key-Id: 65BA331C
+Key-Id: 76BB3C42
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (kfreebsd-i386) 11 Jan 2012 07:13 ║
+║ bedtools 2.16.1-1 (kfreebsd-i386) 16 Mar 2012 12:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: kfreebsd-i386
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid InRelease
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-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://mirror-ubc.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org Release.gpg
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -61,13 +61,16 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-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
+Hit http://mirror-ubc.debian.org sid/contrib Translation-en
+Hit http://mirror-ubc.debian.org sid/main Translation-en
+Hit http://mirror-ubc.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Translation-en
+Hit http://incoming.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org Translation-en
-Fetched 654 kB in 6s (97.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -88,11 +91,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (640 kB/s)
Download complete and in download only mode
Check arch
@@ -112,12 +115,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,38 +129,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
+base-files: already installed (6.7)
base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
-coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
-diffutils: already installed (1:3.2-1)
+coreutils: already installed (8.13-3.1)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.2.1)
+diffutils: already installed (1:3.2-2)
dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
-findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds3-2)
+e2fsprogs: already installed (1.42.1-2)
+findutils: already installed (4.4.2-4)
+freebsd-utils: already installed (9.0-2)
grep: already installed (2.10-1)
-gzip: already installed (1.4-2)
-hostname: already installed (3.09)
+gzip: already installed (1.4-3)
+hostname: already installed (3.11)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+login: already installed (1:4.1.5-1)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
+bsdutils: already installed (1:2.20.1-4)
+util-linux: already installed (2.20.1-4)
libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -167,8 +170,8 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf
python-minimal python2.7 python2.7-minimal
Suggested packages:
@@ -176,59 +179,56 @@ Suggested packages:
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
+ curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 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
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libdb4.8 libffi5 libglib2.0-0 libmagic1 libpipeline1 libsqlite3-0
+ libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python
+ python-minimal python2.7 python2.7-minimal quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-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.
+0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/15.4 MB of archives.
+After this operation, 41.3 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 11527 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-i386.deb) ...
+(Reading database ... 11923 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_kfreebsd-i386.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_kfreebsd-i386.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_kfreebsd-i386.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_kfreebsd-i386.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_kfreebsd-i386.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-i386.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
Selecting previously unselected package libdb4.8.
Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_kfreebsd-i386.deb) ...
-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_2.6.0.2-3_kfreebsd-i386.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_kfreebsd-i386.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_kfreebsd-i386.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-11_kfreebsd-i386.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_kfreebsd-i386.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.2-11_kfreebsd-i386.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext.
@@ -238,53 +238,52 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_kfreebsd-i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_kfreebsd-i386.deb) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.2-11) ...
+Setting up python2.7 (2.7.2-11) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-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
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 kfreebsd-kernel-headers_0.77 libc0.1-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1
+Package versions: apt_0.8.15.10 autotools-dev_20120210.1 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3.1 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.42 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 freebsd-utils_9.0-2 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.10-1 groff-base_1.21-6 gzip_1.4-3 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0-2 kfreebsd-kernel-headers_0.77 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbsd0_0.3.0-2 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc0.1_2.13-27 libc0.1-dev_2.13-27 libcam6_9.0+ds1-1 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_9.0+ds1-1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgnutls26_2.12.17-2 libgomp1_4.6.3-1 libgpg-error0_1.10-3 libgssglue1_0.3-4 libjail1_9.0+ds1-1 libkiconv4_9.0+ds1-1 libkvm0_9.0+ds1-1 libldap-2.4-2_2.4.28-1.1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.12-2 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libpng12-0_1.2.47-1 libprocps0_1:3.3.2-3 libquadmath0_4.6.3-1 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-4 libsbuf6_9.0+ds1-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtasn1-3_2.11-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 login_1:4.1.5-1 lsb-base_3.2+Debian31 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 procps_1:3.3.2-3 psmisc_22.16-1 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-11 python2.7-minimal_2.7.2-11 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -295,12 +294,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -311,24 +310,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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-kfreebsd-i386-Njudl6/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -341,52 +354,44 @@ 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_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -426,143 +431,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -571,59 +571,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -631,6 +629,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -638,83 +642,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.16.1-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0719
+Build finished at 20120316-1221
-bedtools_2.15.0-1_kfreebsd-i386.changes:
+bedtools_2.16.1-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 4c61e91d0123b00aa458bf4efdd149949e774ce0 402204 bedtools_2.15.0-1_kfreebsd-i386.deb
+ cf2e5fce429856d71a47d218357533895a43b37b 443250 bedtools_2.16.1-1_kfreebsd-i386.deb
Checksums-Sha256:
- 2abf1b1251c2005b38adf49c7110ddd84dde20f975e7ebeab8dc5d808655c246 402204 bedtools_2.15.0-1_kfreebsd-i386.deb
+ 1f77d3f0574b1bb4bbe95831613804b2d8e50948f6adb8cba0ae541fa044855e 443250 bedtools_2.16.1-1_kfreebsd-i386.deb
Files:
- 3ba4aae440c04a84ffc031f1a9eaccce 402204 science optional bedtools_2.15.0-1_kfreebsd-i386.deb
+ 7925cc91df148cd76bc4e20158d68c93 443250 science optional bedtools_2.16.1-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_kfreebsd-i386.deb
+bedtools_2.16.1-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 402204 bytes: control archive= 1872 bytes.
+ size 443250 bytes: control archive= 1981 bytes.
875 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1247
+ Installed-Size: 1399
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -730,54 +806,58 @@ bedtools_2.15.0-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:17 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 12:21 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 12:21 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1403068 2012-03-16 12:21 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/mapBed
+-rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:21 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:21 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 12:21 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-03-16 12:21 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-03-16 12:21 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:21 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 12:21 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-03-16 12:21 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-03-16 12:21 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 12:21 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -791,23 +871,23 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1326266009-46743/build/buildd-bedtools_2.15.0-1-kfreebsd-i386-Njudl6
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1331900161-75362/build/buildd-bedtools_2.16.1-1-kfreebsd-i386-MncTMY
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0*
- libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2*
- man-db* mime-support* po-debconf* python* python-minimal* python2.7*
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libdb4.8* libffi5* libglib2.0-0* libmagic1*
+ libpipeline1* libsqlite3-0* libssl1.0.0* libunistring0* libxml2* man-db*
+ mime-support* po-debconf* python* python-minimal* python2.7*
python2.7-minimal* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 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.)
+0 upgraded, 0 newly installed, 27 to remove and 0 not upgraded.
+After this operation, 41.3 MB disk space will be freed.
+(Reading database ... 14015 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -818,10 +898,6 @@ 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 ...
@@ -837,6 +913,8 @@ 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 ...
@@ -859,18 +937,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 62552
-Build-Time: 186
+Build-Space: 72048
+Build-Time: 235
Distribution: sid
-Install-Time: 124
-Job: bedtools_2.15.0-1
+Install-Time: 59
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 337
-Source-Version: 2.15.0-1
-Space: 62552
+Package-Time: 315
+Source-Version: 2.16.1-1
+Space: 72048
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0719
-Build needed 00:05:37, 62552k disc space
-Signature with key '65BA331C' requested:
+Finished at 20120316-1221
+Build needed 00:05:15, 72048k disc space
+Signature with key '76BB3C42' requested:
diff --git a/mips.log b/mips.log
index 651abc3..71a90c8 100644
--- a/mips.log
+++ b/mips.log
@@ -1,68 +1,69 @@
-From buildd2 at lucatelli.debian.org Wed Jan 11 07:45:58 2012
-Return-path: <buildd2 at lucatelli.debian.org>
+From buildd2 at corelli.debian.org Fri Mar 16 12:56:52 2012
+Return-path: <buildd2 at corelli.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at 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])
+ (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
+ id 1S8WiB-0003Ss-UL
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:52 +0000
+Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lucatelli.debian.org,
- EMAIL=hostmaster at lucatelli.debian.org (verified)
+ CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (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>
+ (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
+ id 1S8WiA-0008L9-8R
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:51 +0000
+Received: from buildd2 by corelli.debian.org with local (Exim 4.72)
+ (envelope-from <buildd2 at corelli.debian.org>) id 1S8Wi6-0007Fp-SG
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:56:47 +0000
+Date: Fri, 16 Mar 2012 12:56:46 +0000
+Message-Id: <E1S8Wi6-0007Fp-SG at corelli.debian.org>
+From: buildd on corelli <buildd2 at corelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on mips (dist=sid)
+Subject: Log for successful build of bedtools_2.16.1-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-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
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (mips) 11 Jan 2012 07:08 ║
+║ bedtools 2.16.1-1 (mips) 16 Mar 2012 12:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: mips
-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]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [198 kB]
+Get:2 http://incoming.debian.org unstable InRelease [198 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6213 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
Get:5 http://incoming.debian.org Release [1616 B]
-Get:6 http://incoming.debian.org unstable/main Sources [6000 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [6213 kB]
Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [54.4 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [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]
+Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [99.8 kB]
+Get:9 http://mirror-ubc.debian.org unstable/main mips Packages [5732 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [37.3 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2085 B]
-Ign http://mirror-ubc.debian.org 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 mips Packages [7732 kB]
-Get:15 http://incoming.debian.org unstable/contrib mips Packages [55.7 kB]
+Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2223 B]
+Get:12 http://mirror-ubc.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:13 http://mirror-ubc.debian.org unstable/main Translation-en [3902 kB]
+Get:14 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:15 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:16 http://incoming.debian.org unstable/main mips Packages [5732 kB]
+Get:17 http://incoming.debian.org unstable/contrib mips Packages [37.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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]
+Get:18 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:19 http://incoming.debian.org Sources [58.9 kB]
+Get:20 http://incoming.debian.org Packages [687 kB]
+Get:21 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:22 http://incoming.debian.org unstable/main Translation-en [3902 kB]
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.9 MB in 1min 24s (344 kB/s)
+Fetched 33.3 MB in 1min 23s (399 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (895 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+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 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,37 +123,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, 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 (4.2.1)
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)
+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 (3.06)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-3)
+perl-base: already installed (5.14.2-7)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-26)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1.1 >= 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 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -166,7 +167,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -180,60 +181,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 47 not upgraded.
+Need to get 17.2 MB of archives.
+After this operation, 49.5 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g mips 1:1.2.6.dfsg-2 [85.3 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libncursesw5 mips 5.9-4 [307 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.1-1 [36.7 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libssl1.0.0 mips 1.0.0h-1 [1089 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.10-1 [252 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.30.2-6 [1751 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-7 [859 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.4-2 [139 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libexpat1 mips 2.0.1-7.2 [143 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libdb4.8 mips 4.8.30-11 [661 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.1 [207 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.1-1 [1027 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.10-1 [52.8 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libsqlite3-0 mips 3.7.10-1 [454 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main python2.7-minimal mips 2.7.2-13 [1609 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main python2.7 mips 2.7.2-13 [2580 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-2 [28.6 kB]
+Get:32 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.6.dfsg-2 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.1 MB in 2s (5808 kB/s)
+Fetched 17.2 MB in 3s (5145 kB/s)
+(Reading database ... 10667 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_mips.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10643 files and directories currently installed.)
+(Reading database ... 10667 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_mips.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_mips.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mips.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_mips.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mips.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_mips.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_mips.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mips.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mips.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mips.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mips.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mips.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mips.deb) ...
Selecting previously unselected package libunistring0.
@@ -241,31 +251,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_mips.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_mips.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_mips.deb) ...
+Unpacking file (from .../archives/file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mips.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-8_mips.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-13_mips.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-8_mips.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.2-13_mips.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously unselected package gettext.
@@ -275,59 +283,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_mips.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mips.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-8) ...
-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 python2.7-minimal (2.7.2-13) ...
+Setting up python2.7 (2.7.2-13) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 47 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-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
+Kernel: Linux 3.2.0-0.bpo.1-octeon mips (mips64)
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6-dev_2.13-26 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.4-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgomp1_4.6.2-12 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-13 python2.7-minimal_2.7.2-13 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -338,12 +346,12 @@ Unpack source
─────────────
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: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -354,24 +362,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" 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/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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -384,52 +406,44 @@ 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/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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
+make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -469,143 +483,138 @@ g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -614,59 +623,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -674,6 +681,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -681,83 +694,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd2-bedtools_2.15.0-1-mips-DGAnfo/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd2-bedtools_2.16.1-1-mips-d4xmpl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../bedtools_2.15.0-1_mips.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../bedtools_2.16.1-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0745
+Build finished at 20120316-1256
-bedtools_2.15.0-1_mips.changes:
+bedtools_2.16.1-1_mips.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
+Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 18ab6a1e16b7c6b81e9e55f9796f521e20b4e375 324664 bedtools_2.15.0-1_mips.deb
+ 294633473dfee43e31f80c55eba2198c8f9b1d2d 354186 bedtools_2.16.1-1_mips.deb
Checksums-Sha256:
- 1c3d6f313dc1f80c392a649bc5e7da8be91efd3d7344cb8313c25c623dbd85d8 324664 bedtools_2.15.0-1_mips.deb
+ 0f319d419654b948cc905235c6becc025d3a75c194026367adfb0860c3423234 354186 bedtools_2.16.1-1_mips.deb
Files:
- a1f13a5324b04f5c71b0cf3e060d8ae0 324664 science optional bedtools_2.15.0-1_mips.deb
+ ead6be44f11d8c16cf85f0503f773e94 354186 science optional bedtools_2.16.1-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_mips.deb
+bedtools_2.16.1-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 324664 bytes: control archive= 1872 bytes.
+ size 354186 bytes: control archive= 1981 bytes.
864 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1345
+ Installed-Size: 1503
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -773,7 +858,58 @@ bedtools_2.15.0-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:17 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2012-03-16 12:55 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 1477568 2012-03-16 12:55 ./usr/bin/bedtools
+-rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/nucBed
+-rwxr-xr-x root/root 36 2012-03-16 12:55 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/flankBed
+-rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/mapBed
+-rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/randomBed
+-rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 35 2012-03-16 12:55 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 36 2012-03-16 12:55 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-03-16 12:55 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/expandCols
+-rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 31 2012-03-16 12:55 ./usr/bin/windowBed
+-rwxr-xr-x root/root 34 2012-03-16 12:55 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 29 2012-03-16 12:55 ./usr/bin/slopBed
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 29 2012-03-16 12:55 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:55 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 32 2012-03-16 12:55 ./usr/bin/closestBed
+-rwxr-xr-x root/root 28 2012-03-16 12:55 ./usr/bin/bedToIgv
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -787,7 +923,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-56da54ba-13fe-4f72-8e32-a6c8efd538e7/build/buildd2-bedtools_2.15.0-1-mips-DGAnfo
+Purging /var/lib/schroot/mount/sid-mips-sbuild-badc569c-02d4-48df-8386-c5135e2e7775/build/buildd2-bedtools_2.16.1-1-mips-d4xmpl
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
@@ -797,23 +933,23 @@ Can't open average space db /var/lib/sbuild/avg-build-space
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 67684
-Build-Time: 1976
+Build-Space: 78100
+Build-Time: 2348
Distribution: sid
-Install-Time: 126
-Job: bedtools_2.15.0-1
+Install-Time: 112
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 2233
-Source-Version: 2.15.0-1
-Space: 67684
+Package-Time: 2605
+Source-Version: 2.16.1-1
+Space: 78100
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0745
-Build needed 00:37:13, 67684k disc space
-Signature with key '7A0A8DA2' requested:
+Finished at 20120316-1256
+Build needed 00:43:25, 78100k disc space
+Signature with key 'B5319330' requested:
-From buildd at mayer.debian.org Wed Jan 11 10:31:34 2012
+From buildd at mayer.debian.org Fri Mar 16 12:41:35 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,
@@ -821,60 +957,170 @@ 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 1RkvSw-00038L-4T
- for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:34 +0000
+ id 1S8WTO-0008SW-KI
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:34 +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 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 1RkvSm-0004n8-Ac
- for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:24 +0000
+ id 1S8WTM-0006kt-Sj
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:33 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mayer.debian.org>) id 1S8WTJ-0000nS-NG
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:29 +0000
+Date: Fri, 16 Mar 2012 12:41:29 +0000
+Message-Id: <E1S8WTJ-0000nS-NG at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.16.1-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-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 2.15.0-1 (mipsel) 11 Jan 2012 10:11 ║
+║ bedtools 2.16.1-1 (mipsel) 16 Mar 2012 12:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: mipsel
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Hit http://debian.oregonstate.edu sid InRelease
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release [1616 B]
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
Hit http://debian.oregonstate.edu sid/main TranslationIndex
-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://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://debian.oregonstate.edu sid/main Translation-en
Hit http://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Get: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
+Get:3 http://incoming.debian.org Sources [58.9 kB]
+Get:4 http://incoming.debian.org Packages [687 kB]
+Hit http://incoming.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 602 kB in 3s (196 kB/s)
+Fetched 748 kB in 5s (127 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -886,20 +1132,92 @@ Check APT
─────────
Checking available source versions...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Download source files with APT
──────────────────────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 2s (375 kB/s)
Download complete and in download only mode
Check arch
@@ -912,26 +1230,200 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
Checking for dependency conflicts...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Installing positive dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- 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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Removing negative dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- 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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
@@ -939,73 +1431,221 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-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 (4.2.1)
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)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42.1-2)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.06)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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 (2.13-24)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-27)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-3 >= 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 8.9.14
+Using default version 9.20120312
quilt: missing
-python: already installed (2.7.2-9)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+python: missing
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following 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 gettext intltool-debian libcroco3 libffi5 libglib2.0-0 po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python-minimal python2.7 python2.7-minimal
Suggested packages:
- devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
+ python-doc python-tk python2.7-doc binfmt-support procmail graphviz
default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat gettext intltool-debian libcroco3 libffi5
- libglib2.0-0 po-debconf quilt
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
+ mime-support po-debconf python python-minimal python2.7 python2.7-minimal
+ quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-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.
+0 upgraded, 29 newly installed, 0 to remove and 21 not upgraded.
+Need to get 0 B/16.3 MB of archives.
+After this operation, 47.9 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 11081 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mipsel.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_mipsel.deb) ...
Selecting previously unselected package libffi5.
-(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.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mipsel.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mipsel.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mipsel.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mipsel.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.1-1_mipsel.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_5.10-1_mipsel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mipsel.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_mipsel.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_mipsel.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
@@ -1013,35 +1653,126 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
-Processing triggers for man-db ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mipsel.deb) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-2) ...
-Setting up cdbs (0.4.100) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.1-1) ...
+Building database of manual pages ...
+Setting up file (5.10-1) ...
+Setting up gettext-base (0.18.1.1-5) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
+Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 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
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.4-1
+Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-3 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdevmapper1.02.1_2:1.02.67-2 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-3 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libpng12-0_1.2.47-1 libprocps0_1:3.3.2-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_175-3.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 procps_1:3.3.2-3 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu2 udev_175-3.1 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1051,13 +1782,49 @@ Package versions: apt_0.8.15.9 asciidoc_8.6.6-1 base-files_6.5 base-passwd_3.5.2
Unpack source
─────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1067,25 +1834,75 @@ Check disc space
dpkg-buildpackage
─────────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1098,52 +1915,44 @@ 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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -1183,143 +1992,138 @@ g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -1328,59 +2132,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -1388,6 +2190,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -1395,46 +2203,118 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.15.0-1_mipsel.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.16.1-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-1031
+Build finished at 20120316-1240
-bedtools_2.15.0-1_mipsel.changes:
+bedtools_2.16.1-1_mipsel.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -1442,36 +2322,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- c269d51b5a5d5de03d017dd7ffdff85bdb3065c8 331704 bedtools_2.15.0-1_mipsel.deb
+ d44fe88544215759e97f1f0e02912cb1dd650530 363526 bedtools_2.16.1-1_mipsel.deb
Checksums-Sha256:
- c0390148a76602895228b854f257af4eb0cc4275426a3235ed43163eae716d38 331704 bedtools_2.15.0-1_mipsel.deb
+ 77de6839d9d0bca335452cbcb333518502bd5aad221da61ce914821d075ddd7b 363526 bedtools_2.16.1-1_mipsel.deb
Files:
- 0843ce5200d9df3b741d4f2ed819e888 331704 science optional bedtools_2.15.0-1_mipsel.deb
+ 6fe24a0483cfa020297c9334647f3b95 363526 science optional bedtools_2.16.1-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_mipsel.deb
+bedtools_2.16.1-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 331704 bytes: control archive= 1867 bytes.
+ size 363526 bytes: control archive= 1978 bytes.
866 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1344
+ Installed-Size: 1503
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1487,7 +2367,58 @@ bedtools_2.15.0-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1477568 2012-03-16 12:40 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/mapBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1501,60 +2432,269 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-404e49be-9ffb-4443-8061-ba8fdfd31536/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following 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* 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.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libdb4.8* libexpat1* libffi5*
+ libglib2.0-0* libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0*
+ libunistring0* libxml2* man-db* mime-support* po-debconf* python*
+ python-minimal* python2.7* python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 29 to remove and 21 not upgraded.
+After this operation, 47.9 MB disk space will be freed.
+(Reading database ... 13370 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
+Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libdb4.8 ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libffi5 ...
Purging configuration files for libffi5 ...
-Processing triggers for man-db ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
+Removing libssl1.0.0 ...
+Purging configuration files for libssl1.0.0 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
+Removing zlib1g-dev ...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 67640
-Build-Time: 1119
+Build-Space: 78100
+Build-Time: 1338
Distribution: sid
-Install-Time: 40
-Job: bedtools_2.15.0-1
+Install-Time: 108
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 1191
-Source-Version: 2.15.0-1
-Space: 67640
+Package-Time: 1536
+Source-Version: 2.16.1-1
+Space: 78100
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-1031
-Build needed 00:19:51, 67640k disc space
-Signature with key 'B0903E66' requested:
+Finished at 20120316-1240
+Build needed 00:25:36, 78100k disc space
+Signature with key '8C9FAB20' requested:
diff --git a/mipsel.log b/mipsel.log
index a6dc714..45d687d 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,4 +1,4 @@
-From buildd at mayer.debian.org Wed Jan 11 10:31:34 2012
+From buildd at mayer.debian.org Fri Mar 16 12:41:35 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,
@@ -6,60 +6,170 @@ 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 1RkvSw-00038L-4T
- for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:34 +0000
+ id 1S8WTO-0008SW-KI
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:34 +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 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 1RkvSm-0004n8-Ac
- for logs at buildd.debian.org; Wed, 11 Jan 2012 10:31:24 +0000
+ id 1S8WTM-0006kt-Sj
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:33 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mayer.debian.org>) id 1S8WTJ-0000nS-NG
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:41:29 +0000
+Date: Fri, 16 Mar 2012 12:41:29 +0000
+Message-Id: <E1S8WTJ-0000nS-NG at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.16.1-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-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 2.15.0-1 (mipsel) 11 Jan 2012 10:11 ║
+║ bedtools 2.16.1-1 (mipsel) 16 Mar 2012 12:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: mipsel
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Hit http://debian.oregonstate.edu sid InRelease
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release [1616 B]
Hit http://debian.oregonstate.edu sid/main Sources
Hit http://debian.oregonstate.edu sid/contrib Sources
Hit http://debian.oregonstate.edu sid/main mipsel Packages
Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
Hit http://debian.oregonstate.edu sid/main TranslationIndex
-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://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://debian.oregonstate.edu sid/main Translation-en
Hit http://incoming.debian.org sid/main Sources
Hit http://incoming.debian.org sid/contrib Sources
Hit http://incoming.debian.org sid/main mipsel Packages
Hit http://incoming.debian.org sid/contrib mipsel Packages
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Get: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
+Get:3 http://incoming.debian.org Sources [58.9 kB]
+Get:4 http://incoming.debian.org Packages [687 kB]
+Hit http://incoming.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 602 kB in 3s (196 kB/s)
+Fetched 748 kB in 5s (127 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -71,20 +181,92 @@ Check APT
─────────
Checking available source versions...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Download source files with APT
──────────────────────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 2s (375 kB/s)
Download complete and in download only mode
Check arch
@@ -97,26 +279,200 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
build-essential: already installed (11.5)
-fakeroot: already installed (1.18.1-1)
+fakeroot: already installed (1.18.2-1)
Checking for dependency conflicts...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Installing positive dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- 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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Removing negative dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- 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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
@@ -124,73 +480,221 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-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 (4.2.1)
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)
+dpkg: already installed (1.16.1.2)
+e2fsprogs: already installed (1.42.1-2)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.06)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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 (2.13-24)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-27)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-3 >= 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 8.9.14
+Using default version 9.20120312
quilt: missing
-python: already installed (2.7.2-9)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+python: missing
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+Installing positive dependencies: cdbs debhelper quilt python zlib1g-dev
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following 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 gettext intltool-debian libcroco3 libffi5 libglib2.0-0 po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1 libpipeline1
+ libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db mime-support
+ po-debconf python-minimal python2.7 python2.7-minimal
Suggested packages:
- devscripts dh-make gettext-doc libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
+ python-doc python-tk python2.7-doc binfmt-support procmail graphviz
default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat gettext intltool-debian libcroco3 libffi5
- libglib2.0-0 po-debconf quilt
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdb4.8 libexpat1 libffi5 libglib2.0-0 libmagic1
+ libpipeline1 libsqlite3-0 libssl1.0.0 libunistring0 libxml2 man-db
+ mime-support po-debconf python python-minimal python2.7 python2.7-minimal
+ quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-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.
+0 upgraded, 29 newly installed, 0 to remove and 21 not upgraded.
+Need to get 0 B/16.3 MB of archives.
+After this operation, 47.9 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 11081 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+Selecting previously unselected package libssl1.0.0.
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_mipsel.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_mipsel.deb) ...
Selecting previously unselected package libffi5.
-(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.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_mipsel.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_mipsel.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_mipsel.deb) ...
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_mipsel.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package libdb4.8.
+Unpacking libdb4.8 (from .../libdb4.8_4.8.30-11_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.1-1_mipsel.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_5.10-1_mipsel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_mipsel.deb) ...
+Selecting previously unselected package mime-support.
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
+Selecting previously unselected package python2.7-minimal.
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_mipsel.deb) ...
+Selecting previously unselected package python2.7.
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_mipsel.deb) ...
+Selecting previously unselected package python-minimal.
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
+Selecting previously unselected package python.
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
@@ -198,35 +702,126 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_mipsel.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
-Processing triggers for man-db ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_mipsel.deb) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-2) ...
-Setting up cdbs (0.4.100) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
+Setting up libexpat1 (2.0.1-7.2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up libdb4.8 (4.8.30-11) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.1-1) ...
+Building database of manual pages ...
+Setting up file (5.10-1) ...
+Setting up gettext-base (0.18.1.1-5) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
+update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
+Setting up python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
+Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 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
+Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.4-1
+Package versions: apt_0.8.15.10 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dmsetup_2:1.02.67-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-3 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdevmapper1.02.1_2:1.02.67-2 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-3 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libpng12-0_1.2.47-1 libprocps0_1:3.3.2-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_175-3.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.4-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 procps_1:3.3.2-3 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu2 udev_175-3.1 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -236,13 +831,49 @@ Package versions: apt_0.8.15.9 asciidoc_8.6.6-1 base-files_6.5 base-passwd_3.5.2
Unpack source
─────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -252,25 +883,75 @@ Check disc space
dpkg-buildpackage
─────────────────
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -283,52 +964,44 @@ 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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -368,143 +1041,138 @@ g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -513,59 +1181,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -573,6 +1239,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -580,46 +1252,118 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.15.0-1_mipsel.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.16.1-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-1031
+Build finished at 20120316-1240
-bedtools_2.15.0-1_mipsel.changes:
+bedtools_2.16.1-1_mipsel.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -627,36 +1371,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- c269d51b5a5d5de03d017dd7ffdff85bdb3065c8 331704 bedtools_2.15.0-1_mipsel.deb
+ d44fe88544215759e97f1f0e02912cb1dd650530 363526 bedtools_2.16.1-1_mipsel.deb
Checksums-Sha256:
- c0390148a76602895228b854f257af4eb0cc4275426a3235ed43163eae716d38 331704 bedtools_2.15.0-1_mipsel.deb
+ 77de6839d9d0bca335452cbcb333518502bd5aad221da61ce914821d075ddd7b 363526 bedtools_2.16.1-1_mipsel.deb
Files:
- 0843ce5200d9df3b741d4f2ed819e888 331704 science optional bedtools_2.15.0-1_mipsel.deb
+ 6fe24a0483cfa020297c9334647f3b95 363526 science optional bedtools_2.16.1-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_mipsel.deb
+bedtools_2.16.1-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 331704 bytes: control archive= 1867 bytes.
+ size 363526 bytes: control archive= 1978 bytes.
866 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1344
+ Installed-Size: 1503
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -672,7 +1416,58 @@ bedtools_2.15.0-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2012-03-16 12:40 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 1477568 2012-03-16 12:40 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/closestBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/complementBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/expandCols
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/flankBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/linksBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/mapBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:40 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/nucBed
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 35 2012-03-16 12:40 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 12:40 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/slopBed
+-rwxr-xr-x root/root 29 2012-03-16 12:40 ./usr/bin/sortBed
+-rwxr-xr-x root/root 33 2012-03-16 12:40 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 28 2012-03-16 12:40 ./usr/bin/tagBam
+-rwxr-xr-x root/root 34 2012-03-16 12:40 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 31 2012-03-16 12:40 ./usr/bin/windowBed
+-rwxr-xr-x root/root 36 2012-03-16 12:40 ./usr/bin/windowMaker
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -686,60 +1481,269 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ccaa109b-1773-46f4-b628-50974a12f6a4/build/buildd-bedtools_2.15.0-1-mipsel-0bLs6N
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-404e49be-9ffb-4443-8061-ba8fdfd31536/build/buildd-bedtools_2.16.1-1-mipsel-xSnKZl
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following 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* 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.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libdb4.8* libexpat1* libffi5*
+ libglib2.0-0* libmagic1* libpipeline1* libsqlite3-0* libssl1.0.0*
+ libunistring0* libxml2* man-db* mime-support* po-debconf* python*
+ python-minimal* python2.7* python2.7-minimal* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 29 to remove and 21 not upgraded.
+After this operation, 47.9 MB disk space will be freed.
+(Reading database ... 13370 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
+Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing python ...
+Purging configuration files for python ...
+Removing python2.7 ...
+Purging configuration files for python2.7 ...
+Removing libdb4.8 ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libffi5 ...
Purging configuration files for libffi5 ...
-Processing triggers for man-db ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing python-minimal ...
+Removing python2.7-minimal ...
+Purging configuration files for python2.7-minimal ...
+Removing libssl1.0.0 ...
+Purging configuration files for libssl1.0.0 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing mime-support ...
+Purging configuration files for mime-support ...
+Removing zlib1g-dev ...
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [sid-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [sid-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [sid-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [wheezy-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [wheezy-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [wheezy-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [squeeze-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [squeeze-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 8 [lenny-security-mipsel-sbuild]: Deprecated key 'run-setup-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 9 [lenny-security-mipsel-sbuild]: Deprecated key 'run-exec-scripts' used
+I: This option will be removed in the future; please update your configuration
+W: line 4 [lenny-security-mipsel-sbuild]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 67640
-Build-Time: 1119
+Build-Space: 78100
+Build-Time: 1338
Distribution: sid
-Install-Time: 40
-Job: bedtools_2.15.0-1
+Install-Time: 108
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 1191
-Source-Version: 2.15.0-1
-Space: 67640
+Package-Time: 1536
+Source-Version: 2.16.1-1
+Space: 78100
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-1031
-Build needed 00:19:51, 67640k disc space
-Signature with key 'B0903E66' requested:
+Finished at 20120316-1240
+Build needed 00:25:36, 78100k disc space
+Signature with key '8C9FAB20' requested:
diff --git a/powerpc.log b/powerpc.log
index f1765a9..343b10c 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,4 +1,4 @@
-From buildd at praetorius.debian.org Wed Jan 11 07:15:30 2012
+From buildd at praetorius.debian.org Fri Mar 16 14:20:07 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,
@@ -6,8 +6,8 @@ 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 praetorius.debian.org>)
- id 1RksPC-0007Qk-Ae
- for logs at buildd.debian.org; Wed, 11 Jan 2012 07:15:30 +0000
+ id 1S8Y0l-0004KR-J7
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 14:20:07 +0000
Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
(helo=praetorius.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -15,15 +15,15 @@ Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
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
+ id 1S8Y0k-0005jF-Gs; Fri, 16 Mar 2012 14:20:06 +0000
Received: from buildd by praetorius.debian.org with local (Exim 4.72)
(envelope-from <buildd at praetorius.debian.org>)
- id 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>
+ id 1S8Y0j-0004Ad-FV; Fri, 16 Mar 2012 14:20:05 +0000
+Date: Fri, 16 Mar 2012 14:20:05 +0000
+Message-Id: <E1S8Y0j-0004Ad-FV at praetorius.debian.org>
From: buildd on praetorius <buildd at praetorius.debian.org>
To: wouter at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on powerpc (dist=sid)
+Subject: Log for successful build of bedtools_2.16.1-1 on powerpc (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -31,38 +31,40 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (powerpc) 11 Jan 2012 07:09 ║
+║ bedtools 2.16.1-1 (powerpc) 16 Mar 2012 14:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: powerpc
-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:1 http://ftp.se.debian.org unstable InRelease [198 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [6213 kB]
+Get:3 http://incoming.debian.org unstable InRelease [198 kB]
Get:4 http://ftp.se.debian.org unstable/contrib Sources [54.4 kB]
-Get:5 http://ftp.se.debian.org unstable/non-free Sources [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]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [99.8 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [5823 kB]
+Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [37.1 kB]
Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2085 B]
-Ign http://ftp.se.debian.org unstable/contrib Translation-en
+Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2223 B]
+Get:9 http://ftp.se.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:10 http://ftp.se.debian.org unstable/main Translation-en [3902 kB]
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 [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]
+Get:11 http://incoming.debian.org Release.gpg [836 B]
+Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main powerpc Packages [5823 kB]
+Get:16 http://incoming.debian.org unstable/contrib powerpc Packages [37.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [62.0 kB]
+Get:22 http://incoming.debian.org Packages [695 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 29.2 MB in 15s (1929 kB/s)
+Fetched 33.5 MB in 19s (1730 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +85,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (530 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +109,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 62 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,29 +132,29 @@ 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 (4.4.2-1+b1)
+findutils: already installed (4.4.2-4)
grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.06)
+hostname: already installed (3.10)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.14.2-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-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 (4:4.6.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.2-1 >= 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 (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-24)
+gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -166,7 +168,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -180,60 +182,69 @@ The following NEW packages will be installed:
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.
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 61 not upgraded.
+Need to get 17.6 MB of archives.
After this operation, 48.9 MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org/debian/ unstable/main 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]
+Get:1 http://ftp.se.debian.org/debian/ unstable/main zlib1g powerpc 1:1.2.6.dfsg-2 [84.9 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main libncursesw5 powerpc 5.9-4 [314 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main libssl1.0.0 powerpc 1.0.0h-1 [1133 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.10-1 [255 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.30.2-6 [1800 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-7 [842 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.4-2 [142 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main libexpat1 powerpc 2.0.1-7.2 [138 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main libdb4.8 powerpc 4.8.30-11 [694 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.1 [208 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.1-1 [1055 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.10-1 [52.9 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:19 http://ftp.se.debian.org/debian/ unstable/main libsqlite3-0 powerpc 3.7.10-1 [431 kB]
+Get:20 http://ftp.se.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://ftp.se.debian.org/debian/ unstable/main python2.7-minimal powerpc 2.7.3~rc1-1 [1748 kB]
+Get:22 http://ftp.se.debian.org/debian/ unstable/main python2.7 powerpc 2.7.3~rc1-1 [2618 kB]
+Get:23 http://ftp.se.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://ftp.se.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:27 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:28 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp.se.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-2 [29.1 kB]
+Get:32 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.6.dfsg-2 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.4 MB in 1s (11.0 MB/s)
+Fetched 17.6 MB in 1s (9565 kB/s)
+(Reading database ... 10672 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.3.4.dfsg-3 (using .../zlib1g_1%3a1.2.6.dfsg-2_powerpc.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10681 files and directories currently installed.)
+(Reading database ... 10672 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_powerpc.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_powerpc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_powerpc.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_powerpc.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_powerpc.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_powerpc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_powerpc.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_powerpc.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_powerpc.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_powerpc.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_powerpc.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_powerpc.deb) ...
Selecting previously unselected package libunistring0.
@@ -241,31 +252,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_powerpc.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_powerpc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2_powerpc.deb) ...
+Unpacking file (from .../file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_powerpc.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_powerpc.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_powerpc.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_powerpc.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_powerpc.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously unselected package gettext.
@@ -275,59 +284,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_powerpc.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_powerpc.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 61 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-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
+Toolchain package versions: binutils_2.22-3 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-11 gcc-4.6_4.6.2-11 libc6-dev_2.13-24 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 linux-libc-dev_3.2.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-3 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-11 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-11 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-10 gcc-4.6_4.6.2-11 gcc-4.6-base_4.6.2-11 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-11 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-11 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-11 libstdc++6-4.6-dev_4.6.2-11 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2.1 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-3 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -338,12 +347,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -354,24 +363,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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-powerpc-lGVZ2I/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -384,52 +407,44 @@ 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_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -469,143 +484,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -614,59 +624,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -674,6 +682,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -681,46 +695,118 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-powerpc-pYC95v/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.15.0-1_powerpc.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.16.1-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0715
+Build finished at 20120316-1420
-bedtools_2.15.0-1_powerpc.changes:
+bedtools_2.16.1-1_powerpc.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
@@ -728,36 +814,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 3c8f2451061750c591d1b6ac3b5766f02099b26c 358462 bedtools_2.15.0-1_powerpc.deb
+ 56935389cf63de0f257ae01c49f874072cab5dbe 394204 bedtools_2.16.1-1_powerpc.deb
Checksums-Sha256:
- 1aace34a32f960766fb5f963e9867a44cf900a58f984762a3bdf49eb47cf8dac 358462 bedtools_2.15.0-1_powerpc.deb
+ 477f43437739d7e187998b7713b85fdaa067f39e293baf12db49323d6bfbf117 394204 bedtools_2.16.1-1_powerpc.deb
Files:
- 00c345f6028f37fd21d951a267a61ef5 358462 science optional bedtools_2.15.0-1_powerpc.deb
+ c3c4eefa069d206a4fee80067d1f244d 394204 science optional bedtools_2.16.1-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_powerpc.deb
+bedtools_2.16.1-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 358462 bytes: control archive= 1869 bytes.
+ size 394204 bytes: control archive= 1976 bytes.
867 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1291
+ Installed-Size: 1426
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -773,54 +859,58 @@ bedtools_2.15.0-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/bin/
+-rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/nucBed
+-rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/expandCols
+-rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/mapBed
+-rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/windowBed
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 36 2012-03-16 14:19 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/complementBed
+-rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/closestBed
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 31 2012-03-16 14:19 ./usr/bin/randomBed
+-rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 29 2012-03-16 14:19 ./usr/bin/slopBed
+-rwxr-xr-x root/root 35 2012-03-16 14:19 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 34 2012-03-16 14:19 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/linksBed
+-rwxr-xr-x root/root 29 2012-03-16 14:19 ./usr/bin/sortBed
+-rwxr-xr-x root/root 32 2012-03-16 14:19 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 33 2012-03-16 14:19 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 36 2012-03-16 14:19 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-03-16 14:19 ./usr/bin/flankBed
+-rwxr-xr-x root/root 28 2012-03-16 14:19 ./usr/bin/tagBam
+-rwxr-xr-x root/root 1399248 2012-03-16 14:19 ./usr/bin/bedtools
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2012-03-16 14:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 14:14 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -834,7 +924,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-3dd40f7d-d12c-4b29-9788-1661fd44b9aa/build/buildd-bedtools_2.15.0-1-powerpc-lGVZ2I
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-08cb5b0d-8010-4648-b47b-2b03c27aa4f0/build/buildd-bedtools_2.16.1-1-powerpc-pYC95v
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -842,18 +932,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 73016
-Build-Time: 255
+Build-Space: 84380
+Build-Time: 308
Distribution: sid
Install-Time: 68
-Job: bedtools_2.15.0-1
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 358
-Source-Version: 2.15.0-1
-Space: 73016
+Package-Time: 417
+Source-Version: 2.16.1-1
+Space: 84380
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0715
-Build needed 00:05:58, 73016k disc space
+Finished at 20120316-1420
+Build needed 00:06:57, 84380k disc space
diff --git a/s390.log b/s390.log
index 044daa1..1992c37 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zemlinsky.debian.org Wed Jan 11 07:12:45 2012
+From buildd at zemlinsky.debian.org Fri Mar 16 12:26:44 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,
@@ -6,64 +6,66 @@ 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 zemlinsky.debian.org>)
- id 1RksMX-0007B4-Fz
- for logs at buildd.debian.org; Wed, 11 Jan 2012 07:12:45 +0000
+ id 1S8WF1-0003k3-Mh
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:26:43 +0000
Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zemlinsky.debian.org,
EMAIL=hostmaster at zemlinsky.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1RksMW-0000hB-Oy; Wed, 11 Jan 2012 07:12:44 +0000
+ id 1S8WF0-0005kx-Qb; Fri, 16 Mar 2012 12:26:42 +0000
Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
(envelope-from <buildd at zemlinsky.debian.org>)
- id 1RksMV-0000vt-T3; Wed, 11 Jan 2012 07:12:43 +0000
-Message-Id: <E1RksMV-0000vt-T3 at zemlinsky.debian.org>
+ id 1S8WEz-0002Jz-QQ; Fri, 16 Mar 2012 12:26:41 +0000
+Message-Id: <E1S8WEz-0002Jz-QQ at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 11 Jan 2012 07:12:43 +0000
+Date: Fri, 16 Mar 2012 12:26:41 +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_2.15.0-1 on s390 (dist=sid)
-Key-Id: 1EEA506A
+Subject: Log for successful build of bedtools_2.16.1-1 on s390 (dist=sid)
+Key-Id: E0AC2C92
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (s390) 11 Jan 2012 07:08 ║
+║ bedtools 2.16.1-1 (s390) 16 Mar 2012 12:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: s390
-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]
+Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [198 kB]
+Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [6213 kB]
+Get:3 http://incoming.debian.org unstable InRelease [198 kB]
+Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [54.4 kB]
+Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
+Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390 Packages [5726 kB]
+Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390 Packages [36.7 kB]
Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
-Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2085 B]
-Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2223 B]
+Get:9 http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en [37.1 kB]
+Get:10 http://ftp-stud.hs-esslingen.de unstable/main Translation-en [3902 kB]
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 [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]
+Get:11 http://incoming.debian.org Release.gpg [836 B]
+Get:12 http://incoming.debian.org unstable/main Sources [6213 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:15 http://incoming.debian.org unstable/main s390 Packages [5726 kB]
+Get:16 http://incoming.debian.org unstable/contrib s390 Packages [36.7 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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
+Get:17 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:18 http://incoming.debian.org Release [1616 B]
+Get:19 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:20 http://incoming.debian.org unstable/main Translation-en [3902 kB]
+Get:21 http://incoming.debian.org Sources [59.8 kB]
+Get:22 http://incoming.debian.org Packages [692 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.9 MB in 9s (3034 kB/s)
+Fetched 33.3 MB in 11s (2825 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +86,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (657 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +110,12 @@ 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 48 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 48 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -127,33 +129,33 @@ base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
+debianutils: already installed (4.2.1)
diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.2)
e2fsprogs: already installed (1.42-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.09)
+hostname: already installed (3.11)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-7)
sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+login: already installed (1:4.1.5-1)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
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)
+bsdutils: already installed (1:2.20.1-1.2)
+mount: already installed (2.20.1-1.2)
+util-linux: already installed (2.20.1-1.2)
+libc6-dev: already installed (2.13-26)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -167,7 +169,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -181,60 +183,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 47 not upgraded.
+Need to get 17.9 MB of archives.
+After this operation, 49.4 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390 1:1.2.6.dfsg-2 [89.4 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390 5.9-4 [323 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390 1.0.0h-1 [1226 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390 5.10-1 [259 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390 2.30.2-6 [1875 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390 2.7.8.dfsg-7 [882 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390 0.6.4-2 [149 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390 2.0.1-7.2 [137 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390 4.8.30-11 [700 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390 9.0.1 [213 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390 2.6.1-1 [1068 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390 5.10-1 [53.5 kB]
Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390 3.7.9-2 [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]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390 3.7.10-1 [456 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390 2.7.3~rc1-1 [1699 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390 2.7.3~rc1-1 [2661 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390 0.18.1.1-5 [2073 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390 1.55-2 [29.7 kB]
+Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390 1:1.2.6.dfsg-2 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.7 MB in 2s (8525 kB/s)
+Fetched 17.9 MB in 1s (17.1 MB/s)
+(Reading database ... 10800 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10720 files and directories currently installed.)
+(Reading database ... 10800 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_s390.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_s390.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_s390.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390.deb) ...
Selecting previously unselected package libunistring0.
@@ -242,31 +253,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_s390.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_s390.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_s390.deb) ...
+Unpacking file (from .../archives/file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_s390.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously unselected package gettext.
@@ -276,59 +285,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_s390.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
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 47 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.4-base_4.4.6-14 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-14 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -339,12 +348,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -355,24 +364,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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_2.15.0-1-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -385,52 +408,44 @@ 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_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -470,143 +485,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -615,59 +625,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -675,6 +683,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -682,46 +696,118 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-s390-Z8mhcA/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-s390-ZJY4QX/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0712
+Build finished at 20120316-1226
-bedtools_2.15.0-1_s390.changes:
+bedtools_2.16.1-1_s390.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
@@ -729,36 +815,36 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- e32cd1b12422f648505c07d028c5b161091c6321 353440 bedtools_2.15.0-1_s390.deb
+ a51394a8cee66cc0e0469d100b641b38a89b7d97 388520 bedtools_2.16.1-1_s390.deb
Checksums-Sha256:
- f9d73fcfe29b096b4ad906a81f10b72067f97d97ea0e47520a4f736e23ba553d 353440 bedtools_2.15.0-1_s390.deb
+ 60f37bcf3e7a6ec0ade5d7de8f5d9dd881316edc7f4779f2ee8a4190f27599e1 388520 bedtools_2.16.1-1_s390.deb
Files:
- 22508ed00f7c81d9dff6a28707786112 353440 science optional bedtools_2.15.0-1_s390.deb
+ 8bbfd52d792de3aa5e84e86bbefac711 388520 science optional bedtools_2.16.1-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_s390.deb
+bedtools_2.16.1-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 353440 bytes: control archive= 1871 bytes.
+ size 388520 bytes: control archive= 1975 bytes.
864 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1252
+ Installed-Size: 1394
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -774,54 +860,58 @@ bedtools_2.15.0-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:22 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-03-16 12:26 ./usr/bin/
+-rwxr-xr-x root/root 36 2012-03-16 12:26 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 29 2012-03-16 12:26 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1366148 2012-03-16 12:26 ./usr/bin/bedtools
+-rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/mapBed
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-03-16 12:26 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/flankBed
+-rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/nucBed
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-03-16 12:26 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/expandCols
+-rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/complementBed
+-rwxr-xr-x root/root 31 2012-03-16 12:26 ./usr/bin/randomBed
+-rwxr-xr-x root/root 30 2012-03-16 12:26 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-03-16 12:26 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-03-16 12:26 ./usr/bin/tagBam
+-rwxr-xr-x root/root 35 2012-03-16 12:26 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:26 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-03-16 12:26 ./usr/bin/unionBedGraphs
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -835,7 +925,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-8e9a11ca-c237-49e8-9c2c-7ea133bf8333/build/buildd-bedtools_2.15.0-1-s390-Z8mhcA
+Purging /var/lib/schroot/mount/sid-s390-sbuild-53766b8b-5bdd-44cf-bca9-514ab6d33688/build/buildd-bedtools_2.16.1-1-s390-ZJY4QX
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -843,87 +933,89 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 77652
-Build-Time: 191
+Build-Space: 89552
+Build-Time: 232
Distribution: sid
-Install-Time: 20
-Job: bedtools_2.15.0-1
+Install-Time: 21
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 227
-Source-Version: 2.15.0-1
-Space: 77652
+Package-Time: 272
+Source-Version: 2.16.1-1
+Space: 89552
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-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])
+Finished at 20120316-1226
+Build needed 00:04:32, 89552k disc space
+Signature with key 'E0AC2C92' requested:
+From buildd at zemlinsky.debian.org Fri Mar 16 12:18:42 2012
+Return-path: <buildd at zemlinsky.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 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])
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7G-00029z-7n
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:18:42 +0000
+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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (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>
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7F-00057G-AL; Fri, 16 Mar 2012 12:18:41 +0000
+Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7F-0003Xc-5i; Fri, 16 Mar 2012 12:18:41 +0000
+Message-Id: <E1S8W7F-0003Xc-5i at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 11 Jan 2012 07:15:42 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
+Date: Fri, 16 Mar 2012 12:18:41 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on s390x (dist=sid)
-Key-Id: 96C8554F
+Subject: Log for successful build of bedtools_2.16.1-1 on s390x (dist=sid)
+Key-Id: 6A3F7E2B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (s390x) 11 Jan 2012 07:09 ║
+║ bedtools 2.16.1-1 (s390x) 16 Mar 2012 12:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: s390x
-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]
+Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
+Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
+Hit http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Hit http://ftp-stud.hs-esslingen.de unstable/main Translation-en
+Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get: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]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Get:3 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Hit http://incoming.debian.org unstable/main s390x Packages
+Hit http://incoming.debian.org unstable/contrib s390x Packages
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-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
+Hit http://incoming.debian.org unstable/main TranslationIndex
+Get:4 http://incoming.debian.org Release [1616 B]
+Hit http://incoming.debian.org unstable/contrib Translation-en
+Hit http://incoming.debian.org unstable/main Translation-en
+Get:5 http://incoming.debian.org Sources [58.9 kB]
+Get:6 http://incoming.debian.org Packages [687 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 27.6 MB in 25s (1088 kB/s)
+Fetched 948 kB in 2s (446 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -944,11 +1036,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (611 kB/s)
Download complete and in download only mode
Check arch
@@ -968,12 +1060,12 @@ 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 47 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 47 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -982,14 +1074,14 @@ Checking correctness of dependencies...
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 (2.13-24)
+libc6-dev: already installed (2.13-26)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1+b1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -1003,7 +1095,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -1017,60 +1109,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 46 not upgraded.
+Need to get 18.1 MB of archives.
+After this operation, 51.5 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390x 1:1.2.6.dfsg-2 [91.1 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.0h-1 [1224 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.10-1 [255 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-6 [1867 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-7 [894 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.4-2 [150 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.1 [214 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.1-1 [1070 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.10-1 [53.6 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.10-1 [448 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3~rc1-1 [1744 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3~rc1-1 [2677 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.6.dfsg-2 [217 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.9 MB in 6s (2938 kB/s)
+Fetched 18.1 MB in 1s (9669 kB/s)
+(Reading database ... 10788 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390x.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10708 files and directories currently installed.)
+(Reading database ... 10788 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_s390x.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390x.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390x.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390x.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_s390x.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_s390x.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390x.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390x.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390x.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_s390x.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390x.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
Selecting previously unselected package libunistring0.
@@ -1078,31 +1179,29 @@ 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+b1_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_s390x.deb) ...
Selecting previously unselected package groff-base.
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+b1_s390x.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2+b1_s390x.deb) ...
+Unpacking file (from .../archives/file_5.10-1_s390x.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_s390x.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390x.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390x.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390x.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_s390x.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390x.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
@@ -1112,59 +1211,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_s390x.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390x.deb) ...
Setting up libncursesw5 (5.9-4+b1) ...
-Setting up libpipeline1 (1.2.0-5+b1) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4+b1) ...
Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-4+b1) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5+b1) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3+b1) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.0.2-3+b1) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2+b1) ...
-Setting up file (5.09-2+b1) ...
+Setting up file (5.10-1) ...
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) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15+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+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
+Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-14 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1+b1 man-db_2.6.1-1 mawk_1.3.3-16+b1 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1175,12 +1274,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1191,24 +1290,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1221,52 +1334,44 @@ 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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -1305,148 +1410,143 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -1455,59 +1555,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -1515,6 +1613,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -1522,83 +1626,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0715
+Build finished at 20120316-1218
-bedtools_2.15.0-1_s390x.changes:
+bedtools_2.16.1-1_s390x.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x 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 (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 9b44e0dc102233b93ada99aafbaf8d26c2b8f0cb 399096 bedtools_2.15.0-1_s390x.deb
+ 424cae8f7eead80d7cde6b6e5ff19bbb341002af 439128 bedtools_2.16.1-1_s390x.deb
Checksums-Sha256:
- 32136babe58c75e0ae6d7837a58199e48c7a5d4cea69ff4f966517ba34104558 399096 bedtools_2.15.0-1_s390x.deb
+ 152d71f6e27f61b20bc49d0a888a243dcac5643582a16170670900b3dfd8620d 439128 bedtools_2.16.1-1_s390x.deb
Files:
- 5ba3774a3acd328ac007d5dcfa83f288 399096 science optional bedtools_2.15.0-1_s390x.deb
+ ac4b1186a2ef597687c0e5c823a25624 439128 science optional bedtools_2.16.1-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_s390x.deb
+bedtools_2.16.1-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 399096 bytes: control archive= 1867 bytes.
+ size 439128 bytes: control archive= 1980 bytes.
866 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1436
+ Installed-Size: 1604
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1614,54 +1790,58 @@ bedtools_2.15.0-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:14 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/bin/
+-rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1580616 2012-03-16 12:18 ./usr/bin/bedtools
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/mapBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/flankBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/nucBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/expandCols
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/complementBed
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/randomBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/tagBam
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/unionBedGraphs
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1675,7 +1855,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-2aaa36e6-7015-4003-a01a-abc96f7363b0/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1683,18 +1863,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 108172
-Build-Time: 282
+Build-Space: 125844
+Build-Time: 235
Distribution: sid
-Install-Time: 18
-Job: bedtools_2.15.0-1
+Install-Time: 21
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 344
-Source-Version: 2.15.0-1
-Space: 108172
+Package-Time: 265
+Source-Version: 2.16.1-1
+Space: 125844
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0715
-Build needed 00:05:44, 108172k disc space
-Signature with key '96C8554F' requested:
+Finished at 20120316-1218
+Build needed 00:04:25, 125844k disc space
+Signature with key '6A3F7E2B' requested:
diff --git a/s390x.log b/s390x.log
index b0a280a..c637308 100644
--- a/s390x.log
+++ b/s390x.log
@@ -1,69 +1,71 @@
-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 buildd at zemlinsky.debian.org Fri Mar 16 12:18:42 2012
+Return-path: <buildd at zemlinsky.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 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])
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7G-00029z-7n
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 12:18:42 +0000
+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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RksPP-0000rQ-6u; Wed, 11 Jan 2012 07:15:43 +0000
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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>
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7F-00057G-AL; Fri, 16 Mar 2012 12:18:41 +0000
+Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1S8W7F-0003Xc-5i; Fri, 16 Mar 2012 12:18:41 +0000
+Message-Id: <E1S8W7F-0003Xc-5i at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 11 Jan 2012 07:15:42 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
+Date: Fri, 16 Mar 2012 12:18:41 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.15.0-1 on s390x (dist=sid)
-Key-Id: 96C8554F
+Subject: Log for successful build of bedtools_2.16.1-1 on s390x (dist=sid)
+Key-Id: 6A3F7E2B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (s390x) 11 Jan 2012 07:09 ║
+║ bedtools 2.16.1-1 (s390x) 16 Mar 2012 12:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: s390x
-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]
+Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [99.8 kB]
+Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
+Hit http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Hit http://ftp-stud.hs-esslingen.de unstable/main Translation-en
+Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get: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]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Get:3 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Hit http://incoming.debian.org unstable/main s390x Packages
+Hit http://incoming.debian.org unstable/contrib s390x Packages
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-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
+Hit http://incoming.debian.org unstable/main TranslationIndex
+Get:4 http://incoming.debian.org Release [1616 B]
+Hit http://incoming.debian.org unstable/contrib Translation-en
+Hit http://incoming.debian.org unstable/main Translation-en
+Get:5 http://incoming.debian.org Sources [58.9 kB]
+Get:6 http://incoming.debian.org Packages [687 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 27.6 MB in 25s (1088 kB/s)
+Fetched 948 kB in 2s (446 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +86,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 1s (611 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +110,12 @@ 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 47 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 47 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,14 +124,14 @@ Checking correctness of dependencies...
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 (2.13-24)
+libc6-dev: already installed (2.13-26)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1+b1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -143,7 +145,7 @@ The following extra packages will be installed:
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
+ python2.7-minimal zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
@@ -157,60 +159,69 @@ The following NEW packages will be installed:
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]
+The following packages will be upgraded:
+ zlib1g
+1 upgraded, 32 newly installed, 0 to remove and 46 not upgraded.
+Need to get 18.1 MB of archives.
+After this operation, 51.5 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g s390x 1:1.2.6.dfsg-2 [91.1 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncursesw5 s390x 5.9-4+b1 [326 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libssl1.0.0 s390x 1.0.0h-1 [1224 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.10-1 [255 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4+b1 [235 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-6 [1867 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-7 [894 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.4-2 [150 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libexpat1 s390x 2.0.1-7.2 [141 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libdb4.8 s390x 4.8.30-11 [714 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.1 [214 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6+b1 [1184 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.1-1 [1070 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.10-1 [53.6 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5+b1 [157 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libsqlite3-0 s390x 3.7.10-1 [448 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7-minimal s390x 2.7.3~rc1-1 [1744 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python2.7 s390x 2.7.3~rc1-1 [2677 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5+b1 [2163 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:30 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:31 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-2 [30.4 kB]
+Get:32 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:33 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.6.dfsg-2 [217 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.9 MB in 6s (2938 kB/s)
+Fetched 18.1 MB in 1s (9669 kB/s)
+(Reading database ... 10788 files and directories currently installed.)
+Preparing to replace zlib1g 1:1.2.6.dfsg-1 (using .../zlib1g_1%3a1.2.6.dfsg-2_s390x.deb) ...
+Unpacking replacement zlib1g ...
+Setting up zlib1g (1:1.2.6.dfsg-2) ...
Selecting previously unselected package libncursesw5.
-(Reading database ... 10708 files and directories currently installed.)
+(Reading database ... 10788 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4+b1_s390x.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5+b1_s390x.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_s390x.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_s390x.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_s390x.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_s390x.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4+b1_s390x.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4+b1_s390x.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_s390x.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_s390x.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_s390x.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2+b1_s390x.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_s390x.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_s390x.deb) ...
Selecting previously unselected package libunistring0.
@@ -218,31 +229,29 @@ 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+b1_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_s390x.deb) ...
Selecting previously unselected package groff-base.
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+b1_s390x.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2+b1_s390x.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.09-2+b1_s390x.deb) ...
+Unpacking file (from .../archives/file_5.10-1_s390x.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+b1_s390x.deb) ...
Selecting previously unselected package libsqlite3-0.
-Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.9-2_s390x.deb) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_s390x.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_s390x.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_s390x.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_s390x.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_s390x.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package gettext.
@@ -252,59 +261,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_s390x.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b1_s390x.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_s390x.deb) ...
Setting up libncursesw5 (5.9-4+b1) ...
-Setting up libpipeline1 (1.2.0-5+b1) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4+b1) ...
Setting up libffi5 (3.0.10-3+b1) ...
-Setting up libglib2.0-0 (2.30.2-4+b1) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5+b1) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3+b1) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6+b1) ...
-Setting up man-db (2.6.0.2-3+b1) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2+b1) ...
-Setting up file (5.09-2+b1) ...
+Setting up file (5.10-1) ...
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) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15+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+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b1) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-14 gcc-4.6_4.6.2-14 libc6-dev_2.13-26 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 linux-libc-dev_3.2.6-1
+Package versions: apt_0.8.15.9+b1 base-files_6.5+b1 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3+b1 cpp_4:4.6.2-4 cpp-4.6_4.6.2-14 dash_0.5.7-2+b1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1+b1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-1+b1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-14 gcc_4:4.6.2-4 gcc-4.6_4.6.2-14 gcc-4.6-base_4.6.2-14 gettext_0.18.1.1-5+b1 gettext-base_0.18.1.1-5+b1 gnupg_1.4.11-3+b1 gpgv_1.4.11-3+b1 grep_2.10-1 groff-base_1.21-6+b1 gzip_1.4-2+b1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-26 libc-dev-bin_2.13-26 libc6_2.13-26 libc6-dev_2.13-26 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3+b1 libgc1c2_1:7.1-8+b1 libgcc1_1:4.6.2-14 libgdbm3_1.8.3-10+b1 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.2-14 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3+b1 libmagic1_5.10-1 libmount1_2.20.1-1.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-3+b1 libncurses5_5.9-4+b1 libncursesw5_5.9-4+b1 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4+b1 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.0-4.1 libsemanage-common_2.1.0-2 libsemanage1_2.1.0-2 libsepol1_2.1.0-1.2 libslang2_2.2.4-6 libsqlite3-0_3.7.10-1 libss2_1.42-1 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.2-14 libstdc++6-4.6-dev_4.6.2-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4+b1 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2-28.1 make_3.81-8.1+b1 man-db_2.6.1-1 mawk_1.3.3-16+b1 mime-support_3.52-1 mount_2.20.1-1.2 multiarch-support_2.13-26 ncurses-base_5.9-4 ncurses-bin_5.9-4+b1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-7 perl-base_5.14.2-7 perl-modules_5.14.2-7 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9+b1 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3+b1 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -315,12 +324,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -331,24 +340,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -361,52 +384,44 @@ 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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -445,148 +460,143 @@ src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and
* compiling TcpSocketEngine_unix_p.cpp
* compiling TcpSocket_p.cpp
src/api/internal/io/TcpSocket_p.cpp: In member function 'std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)':
-src/api/internal/io/TcpSocket_p.cpp:335:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
+src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
* compiling SamFormatParser_p.cpp
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -595,59 +605,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -655,6 +663,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -662,83 +676,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ gzip -9nf usr/share/doc/bedtools/changelog.Debian usr/share/doc/bedtools/changelog
+ cd '/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-s390x-6s5uie/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-s390x-CaK8CS/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_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-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.16.1-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0715
+Build finished at 20120316-1218
-bedtools_2.15.0-1_s390x.changes:
+bedtools_2.16.1-1_s390x.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: s390x
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x 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 (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- 9b44e0dc102233b93ada99aafbaf8d26c2b8f0cb 399096 bedtools_2.15.0-1_s390x.deb
+ 424cae8f7eead80d7cde6b6e5ff19bbb341002af 439128 bedtools_2.16.1-1_s390x.deb
Checksums-Sha256:
- 32136babe58c75e0ae6d7837a58199e48c7a5d4cea69ff4f966517ba34104558 399096 bedtools_2.15.0-1_s390x.deb
+ 152d71f6e27f61b20bc49d0a888a243dcac5643582a16170670900b3dfd8620d 439128 bedtools_2.16.1-1_s390x.deb
Files:
- 5ba3774a3acd328ac007d5dcfa83f288 399096 science optional bedtools_2.15.0-1_s390x.deb
+ ac4b1186a2ef597687c0e5c823a25624 439128 science optional bedtools_2.16.1-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_s390x.deb
+bedtools_2.16.1-1_s390x.deb
───────────────────────────
new debian package, version 2.0.
- size 399096 bytes: control archive= 1867 bytes.
+ size 439128 bytes: control archive= 1980 bytes.
866 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1436
+ Installed-Size: 1604
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -754,54 +840,58 @@ bedtools_2.15.0-1_s390x.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 12:14 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-03-16 12:18 ./usr/bin/
+-rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/slopBed
+-rwxr-xr-x root/root 1580616 2012-03-16 12:18 ./usr/bin/bedtools
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/mapBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 29 2012-03-16 12:18 ./usr/bin/sortBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/flankBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bedpeToBam
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/windowBed
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/nucBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 36 2012-03-16 12:18 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/expandCols
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/complementBed
+-rwxr-xr-x root/root 31 2012-03-16 12:18 ./usr/bin/randomBed
+-rwxr-xr-x root/root 30 2012-03-16 12:18 ./usr/bin/linksBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 32 2012-03-16 12:18 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 28 2012-03-16 12:18 ./usr/bin/tagBam
+-rwxr-xr-x root/root 35 2012-03-16 12:18 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 12:18 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 34 2012-03-16 12:18 ./usr/bin/unionBedGraphs
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -815,7 +905,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-2aaa36e6-7015-4003-a01a-abc96f7363b0/build/buildd-bedtools_2.16.1-1-s390x-CaK8CS
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -823,18 +913,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 108172
-Build-Time: 282
+Build-Space: 125844
+Build-Time: 235
Distribution: sid
-Install-Time: 18
-Job: bedtools_2.15.0-1
+Install-Time: 21
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 344
-Source-Version: 2.15.0-1
-Space: 108172
+Package-Time: 265
+Source-Version: 2.16.1-1
+Space: 125844
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0715
-Build needed 00:05:44, 108172k disc space
-Signature with key '96C8554F' requested:
+Finished at 20120316-1218
+Build needed 00:04:25, 125844k disc space
+Signature with key '6A3F7E2B' requested:
diff --git a/sparc.log b/sparc.log
index 8f58ede..8299a1a 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,69 +1,72 @@
-From buildd at lebrun.debian.org Wed Jan 11 07:34:30 2012
-Return-path: <buildd at lebrun.debian.org>
+From buildd at schroeder.debian.org Fri Mar 16 13:41:03 2012
+Return-path: <buildd at schroeder.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from 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 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])
+ (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
+ id 1S8XOx-0001qS-BO
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 13:41:03 +0000
+Received: from schroeder.debian.org ([193.198.184.11])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
+ CN=schroeder.debian.org,
+ EMAIL=hostmaster at schroeder.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1RkshX-0004Nk-87
- for logs at buildd.debian.org; Wed, 11 Jan 2012 07:34:27 +0000
-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>
+ (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
+ id 1S8XOw-0002w1-AP
+ for logs at buildd.debian.org; Fri, 16 Mar 2012 13:41:02 +0000
+Received: from buildd by schroeder.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at schroeder.debian.org>)
+ id 1S8XOu-00029p-FT; Fri, 16 Mar 2012 13:41:00 +0000
+Message-Id: <E1S8XOu-00029p-FT at schroeder.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-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
+Date: Fri, 16 Mar 2012 13:41:00 +0000
+From: buildd on schroeder <buildd at schroeder.debian.org>
+To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
+Subject: Log for successful build of bedtools_2.16.1-1 on sparc (dist=sid)
+Key-Id: 24E4F805
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.15.0-1 (sparc) 11 Jan 2012 07:21 ║
+║ bedtools 2.16.1-1 (sparc) 16 Mar 2012 13:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.15.0-1
-Source Version: 2.15.0-1
+Version: 2.16.1-1
+Source Version: 2.16.1-1
Architecture: sparc
-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]
+Get:1 http://ftp.hr.debian.org unstable InRelease [198 kB]
+Get:2 http://incoming.debian.org unstable InRelease [198 kB]
+Get:3 http://ftp.hr.debian.org unstable/main Sources [6213 kB]
+Get:4 http://ftp.hr.debian.org unstable/contrib Sources [54.4 kB]
+Get:5 http://ftp.hr.debian.org unstable/non-free Sources [99.8 kB]
Ign http://incoming.debian.org InRelease
Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://debian.carnet.hr unstable/main sparc Packages [7791 kB]
+Get:7 http://ftp.hr.debian.org unstable/main sparc Packages [5777 kB]
Get:8 http://incoming.debian.org Release [1616 B]
-Get:9 http://incoming.debian.org unstable/main Sources [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]
+Get:9 http://incoming.debian.org unstable/main Sources [6213 kB]
+Get:10 http://ftp.hr.debian.org unstable/contrib sparc Packages [36.9 kB]
+Ign http://ftp.hr.debian.org unstable/contrib TranslationIndex
+Get:11 http://ftp.hr.debian.org unstable/main TranslationIndex [2223 B]
+Get:12 http://ftp.hr.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:13 http://ftp.hr.debian.org unstable/main Translation-en [3902 kB]
+Get:14 http://incoming.debian.org unstable/contrib Sources [54.4 kB]
+Get:15 http://incoming.debian.org unstable/non-free Sources [99.8 kB]
+Get:16 http://incoming.debian.org unstable/main sparc Packages [5777 kB]
+Get:17 http://incoming.debian.org unstable/contrib sparc Packages [36.9 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get: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]
+Get:18 http://incoming.debian.org unstable/main TranslationIndex [2223 B]
+Get:19 http://incoming.debian.org Sources [61.1 kB]
+Get:20 http://incoming.debian.org Packages [697 kB]
+Get:21 http://incoming.debian.org unstable/contrib Translation-en [37.1 kB]
+Get:22 http://incoming.debian.org unstable/main Translation-en [3902 kB]
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 29.0 MB in 32s (900 kB/s)
+Fetched 33.4 MB in 34s (972 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +87,11 @@ 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 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)
+Need to get 985 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (dsc) [1975 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (tar) [978 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.16.1-1 (diff) [5035 B]
+Fetched 985 kB in 3s (327 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +111,12 @@ 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 10 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 10 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,39 +125,39 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, python, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
+base-files: already installed (6.7)
base-passwd: already installed (3.5.24)
bash: already installed (4.2-1)
coreutils: already installed (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.1)
-diffutils: already installed (1:3.2-1)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.2.1)
+diffutils: already installed (1:3.2-2)
dpkg: already installed (1.16.1.2)
-e2fsprogs: already installed (1.42-1)
+e2fsprogs: already installed (1.42.1-2)
findutils: already installed (4.4.2-4)
grep: already installed (2.10-1)
gzip: already installed (1.4-2)
-hostname: already installed (3.09)
+hostname: already installed (3.11)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.14.2-6)
+perl-base: already installed (5.14.2-9)
sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-18)
-sysvinit: already installed (2.88dsf-18)
+login: already installed (1:4.1.5-1)
+sysvinit-utils: already installed (2.88dsf-22)
+sysvinit: already installed (2.88dsf-22)
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)
+bsdutils: already installed (1:2.20.1-4)
+mount: already installed (2.20.1-4)
+util-linux: already installed (2.20.1-4)
+libc6-dev: already installed (2.13-27)
+libc6-dev-sparc64: already installed (2.13-27)
gcc: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.2 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.14
+Using default version 9.20120312
quilt: missing
python: missing
zlib1g-dev: missing
@@ -182,60 +185,62 @@ The following NEW packages will be installed:
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.
+0 upgraded, 32 newly installed, 0 to remove and 10 not upgraded.
+Need to get 16.9 MB of archives.
After this operation, 47.8 MB of additional disk space will be used.
-Get:1 http://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]
+Get:1 http://ftp.hr.debian.org/debian/ unstable/main libncursesw5 sparc 5.9-4 [302 kB]
+Get:2 http://ftp.hr.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
+Get:3 http://ftp.hr.debian.org/debian/ unstable/main libssl1.0.0 sparc 1.0.0h-1 [1052 kB]
+Get:4 http://ftp.hr.debian.org/debian/ unstable/main libmagic1 sparc 5.10-1 [248 kB]
+Get:5 http://ftp.hr.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:6 http://ftp.hr.debian.org/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:7 http://ftp.hr.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.30.2-6 [1694 kB]
+Get:8 http://ftp.hr.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-7 [819 kB]
+Get:9 http://ftp.hr.debian.org/debian/ unstable/main libcroco3 sparc 0.6.4-2 [135 kB]
+Get:10 http://ftp.hr.debian.org/debian/ unstable/main libexpat1 sparc 2.0.1-7.2 [128 kB]
+Get:11 http://ftp.hr.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:12 http://ftp.hr.debian.org/debian/ unstable/main libdb4.8 sparc 4.8.30-11 [639 kB]
+Get:13 http://ftp.hr.debian.org/debian/ unstable/main bsdmainutils sparc 9.0.1 [205 kB]
+Get:14 http://ftp.hr.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:15 http://ftp.hr.debian.org/debian/ unstable/main man-db sparc 2.6.1-1 [1039 kB]
+Get:16 http://ftp.hr.debian.org/debian/ unstable/main file sparc 5.10-1 [52.5 kB]
+Get:17 http://ftp.hr.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:18 http://ftp.hr.debian.org/debian/ unstable/main libsqlite3-0 sparc 3.7.10-1 [406 kB]
+Get:19 http://ftp.hr.debian.org/debian/ unstable/main mime-support all 3.52-1 [35.5 kB]
+Get:20 http://ftp.hr.debian.org/debian/ unstable/main python2.7-minimal sparc 2.7.3~rc1-1 [1600 kB]
+Get:21 http://ftp.hr.debian.org/debian/ unstable/main python2.7 sparc 2.7.3~rc1-1 [2588 kB]
+Get:22 http://ftp.hr.debian.org/debian/ unstable/main python-minimal all 2.7.2-10 [40.0 kB]
+Get:23 http://ftp.hr.debian.org/debian/ unstable/main python all 2.7.2-10 [177 kB]
+Get:24 http://ftp.hr.debian.org/debian/ unstable/main cdbs all 0.4.109 [79.4 kB]
+Get:25 http://ftp.hr.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:26 http://ftp.hr.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
+Get:27 http://ftp.hr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:28 http://ftp.hr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:29 http://ftp.hr.debian.org/debian/ unstable/main debhelper all 9.20120312 [694 kB]
+Get:30 http://ftp.hr.debian.org/debian/ unstable/main diffstat sparc 1.55-2 [28.4 kB]
+Get:31 http://ftp.hr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:32 http://ftp.hr.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.6.dfsg-2 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 16.8 MB in 12s (1361 kB/s)
+Fetched 16.9 MB in 12s (1308 kB/s)
Selecting previously unselected package libncursesw5.
-(Reading database ... 10998 files and directories currently installed.)
+(Reading database ... 11074 files and directories currently installed.)
Unpacking libncursesw5 (from .../libncursesw5_5.9-4_sparc.deb) ...
Selecting previously unselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_sparc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.1-1_sparc.deb) ...
Selecting previously unselected package libssl1.0.0.
-Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_sparc.deb) ...
+Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0h-1_sparc.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.10-1_sparc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_sparc.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_sparc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_sparc.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_sparc.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_sparc.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.4-2_sparc.deb) ...
Selecting previously unselected package libexpat1.
Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_sparc.deb) ...
Selecting previously unselected package libunistring0.
@@ -243,31 +248,29 @@ 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) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_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_2.6.0.2-3_sparc.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.1-1_sparc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_sparc.deb) ...
+Unpacking file (from .../archives/file_5.10-1_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) ...
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.10-1_sparc.deb) ...
Selecting previously unselected package mime-support.
-Unpacking mime-support (from .../mime-support_3.51-1_all.deb) ...
+Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ...
Selecting previously unselected package python2.7-minimal.
-Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.2-10_sparc.deb) ...
+Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc1-1_sparc.deb) ...
Selecting previously unselected package python2.7.
-Unpacking python2.7 (from .../python2.7_2.7.2-10_sparc.deb) ...
+Unpacking python2.7 (from .../python2.7_2.7.3~rc1-1_sparc.deb) ...
Selecting previously unselected package python-minimal.
-Unpacking python-minimal (from .../python-minimal_2.7.2-9_all.deb) ...
+Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ...
Selecting previously unselected package python.
-Unpacking python (from .../python_2.7.2-9_all.deb) ...
+Unpacking python (from .../python_2.7.2-10_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.100_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.109_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously unselected package gettext.
@@ -277,59 +280,59 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120312_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-2_sparc.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.50-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_sparc.deb) ...
Setting up libncursesw5 (5.9-4) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libssl1.0.0 (1.0.0e-3) ...
+Setting up libpipeline1 (1.2.1-1) ...
+Setting up libssl1.0.0 (1.0.0h-1) ...
+Setting up libmagic1 (5.10-1) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5.1) ...
-Setting up libcroco3 (0.6.2-2) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
+Setting up libcroco3 (0.6.4-2) ...
Setting up libexpat1 (2.0.1-7.2) ...
Setting up libunistring0 (0.9.3-5) ...
Setting up libdb4.8 (4.8.30-11) ...
-Setting up bsdmainutils (8.2.3) ...
+Setting up bsdmainutils (9.0.1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-3) ...
+Setting up man-db (2.6.1-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.09-2) ...
-Setting up file (5.09-2) ...
+Setting up file (5.10-1) ...
Setting up gettext-base (0.18.1.1-5) ...
-Setting up libsqlite3-0 (3.7.9-2) ...
-Setting up mime-support (3.51-1) ...
+Setting up libsqlite3-0 (3.7.10-1) ...
+Setting up mime-support (3.52-1) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode.
-Setting up python2.7-minimal (2.7.2-10) ...
-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 python2.7-minimal (2.7.3~rc1-1) ...
+Setting up python2.7 (2.7.3~rc1-1) ...
+Setting up python-minimal (2.7.2-10) ...
+Setting up python (2.7.2-10) ...
+Setting up cdbs (0.4.109) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (8.9.14) ...
+Setting up debhelper (9.20120312) ...
Setting up diffstat (1.55-2) ...
-Setting up quilt (0.50-2) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev (1:1.2.6.dfsg-2) ...
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 10 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-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
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.3-1 gcc-4.6_4.6.3-1 libc6-dev_2.13-27 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 linux-libc-dev_3.2.6-1
+Package versions: apt_0.8.15.9 base-files_6.7 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5 bzip2_1.0.6-1 cdbs_0.4.109 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1 dash_0.5.7-3 debconf_1.5.41 debfoster_2.7-1.1 debhelper_9.20120312 debian-archive-keyring_2010.08.28 debianutils_4.2.1 diffstat_1.55-2 diffutils_1:3.2-2 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42.1-2 e2fsprogs_1.42.1-2 fakeroot_1.18.2-1 file_5.10-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1 gcc_4:4.6.2-4 gcc-4.6_4.6.3-1 gcc-4.6-base_4.6.3-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.12-3 gpgv_1.4.12-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-27 libc-dev-bin_2.13-27 libc6_2.13-27 libc6-dev_2.13-27 libc6-dev-sparc64_2.13-27 libc6-sparc64_2.13-27 libclass-isa-perl_0.36-3 libcomerr2_1.42.1-2 libcroco3_0.6.4-2 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.3-1 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.6.3-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.10-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libsqlite3-0_3.7.10-1 libss2_1.42.1-2 libssl1.0.0_1.0.0h-1 libstdc++6_4.6.3-1 libstdc++6-4.6-dev_4.6.3-1 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.6-1 login_1:4.1.5-1 lsb-base_3.2+Debian29 make_3.81-8.1 man-db_2.6.1-1 mawk_1.3.3-16 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-27 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc1-1 python2.7-minimal_2.7.3~rc1-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -340,12 +343,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Jan 11 06:48:11 2012 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Mar 16 11:42:52 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_2.15.0-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.15.0
-dpkg-source: info: unpacking bedtools_2.15.0.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.15.0-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.16.1-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.16.1
+dpkg-source: info: unpacking bedtools_2.16.1.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.16.1-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -356,24 +359,38 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.15.0-1
- dpkg-source --before-build bedtools-2.15.0
+dpkg-buildpackage: source version 2.16.1-1
+ dpkg-source --before-build bedtools-2.16.1
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -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-sparc-zDCFqL/bedtools-2.15.0'
-Cleaning up.
-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="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+ * Cleaning-up BamTools API
+ * Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
dh_clean
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} \; \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \)
+ rm -f *-stamp
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
if [ -d "." ]; then \
- 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 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -386,52 +403,44 @@ 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_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
make[1]: Nothing to be done for `reverse-config'.
-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
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
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_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
make[1]: Nothing to be done for `update-config'.
-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_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
-[ -d obj ] || mkdir -p obj
-[ -d bin ] || mkdir -p bin
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro"
+make[1]: Entering directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
Building BEDTools:
=========================================================
-- Building in src/utils/lineFileUtilities
- * compiling lineFileUtilities.cpp
-
+DETECTED_VERSION = v2.16.1
+CURRENT_VERSION = v2.16.1
+ * Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
-
+- Building in src/utils/version
+ * compiling version.cpp
- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
-
- Building in src/utils/chromsweep
* compiling chromsweep.cpp
-
- Building in src/utils/gzstream
g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
-
- Building in src/utils/fileType
* compiling fileType.cpp
-
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
-
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
-
- Building in src/utils/tabFile
* compiling tabFile.cpp
-
- Building in src/utils/BamTools
* compiling BamAlignment.cpp
* compiling BamMultiReader.cpp
@@ -471,143 +480,138 @@ g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-securit
* compiling SamFormatPrinter_p.cpp
* compiling SamHeaderValidator_p.cpp
* compiling BamException_p.cpp
-[ -d lib ] || mkdir -p lib
-[ -d include ] || mkdir -p include
-[ -d include/api ] || mkdir -p include/api
-[ -d include/shared ] || mkdir -p include/shared
- * linking libbamtools.a
+ * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
-
+ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
-
+ * compiling BamAncillary.cpp
+- Building in src/utils/BlockedIntervals
+ * compiling BlockedIntervals.cpp
+ * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
* compiling Fasta.cpp
Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
* compiling split.cpp
-
+ * compiling split.cpp
+- Building in src/utils/VectorOps
+ * compiling VectorOps.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
-
- Building in src/annotateBed
* compiling annotateMain.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
* compiling annotateBed.cpp
-
- Building in src/bamToBed
* compiling bamToBed.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:74:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
-
+- Building in src/bamToFastq
+ * compiling bamToFastqMain.cpp
+bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
+bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
+ * compiling bamToFastq.cpp
- Building in src/bedToBam
* compiling bedToBam.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedpeToBam
* compiling bedpeToBam.cpp
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
-
- Building in src/bedToIgv
* compiling bedToIgv.cpp
-
- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
-
- Building in src/closestBed
* compiling closestMain.cpp
* compiling closestBed.cpp
-
- Building in src/clusterBed
* compiling clusterMain.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling clusterBed.cpp
-
- Building in src/complementBed
* compiling complementMain.cpp
* compiling complementBed.cpp
-
- Building in src/coverageBed
* compiling coverageMain.cpp
* compiling coverageBed.cpp
-
+- Building in src/expand
+ * compiling expand.cpp
- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
* compiling fastaFromBed.cpp
-
- Building in src/flankBed
* compiling flankBedMain.cpp
* compiling flankBed.cpp
-
- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
* compiling genomeCoverageBed.cpp
-
- Building in src/getOverlap
* compiling getOverlap.cpp
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-
- Building in src/groupBy
* compiling groupBy.cpp
groupBy.cpp: In function 'int groupby_main(int, char**)':
-groupBy.cpp:84:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
-
+groupBy.cpp:64:10: warning: variable 'haveOps' set but not used [-Wunused-but-set-variable]
- Building in src/intersectBed
* compiling intersectMain.cpp
* compiling intersectBed.cpp
-
- Building in src/linksBed
* compiling linksMain.cpp
* compiling linksBed.cpp
-
- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
* compiling maskFastaFromBed.cpp
-
+- Building in src/mapBed
+ * compiling mapMain.cpp
+mapMain.cpp: In function 'int map_main(int, char**)':
+mapMain.cpp:44:10: warning: variable 'haveColumn' set but not used [-Wunused-but-set-variable]
+mapMain.cpp:45:10: warning: variable 'haveOperation' set but not used [-Wunused-but-set-variable]
+ * compiling mapBed.cpp
- Building in src/mergeBed
* compiling mergeMain.cpp
mergeMain.cpp: In function 'int merge_main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
-
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
* compiling multiBamCov.cpp
-
- Building in src/multiIntersectBed
- * compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling multiIntersectBed.cpp
- Building in src/nucBed
* compiling nucBedMain.cpp
* compiling nucBed.cpp
-
- Building in src/pairToBed
* compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling pairToBed.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
-pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
-pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
-
+pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
- Building in src/pairToPair
* compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
@@ -616,59 +620,57 @@ pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wu
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
-
+- Building in src/randomBed
+ * compiling randomBedMain.cpp
+ * compiling randomBed.cpp
- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
* compiling shuffleBed.cpp
-
- Building in src/slopBed
* compiling slopBedMain.cpp
* compiling slopBed.cpp
-
- Building in src/sortBed
* compiling sortMain.cpp
* compiling sortBed.cpp
-
- Building in src/subtractBed
* compiling subtractMain.cpp
subtractMain.cpp: In function 'int subtract_main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling subtractBed.cpp
-
- Building in src/tagBam
* compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int tagbam_main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
* compiling tagBam.cpp
-
- Building in src/unionBedGraphs
- * compiling unionBedGraphs.cpp
* compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
-
+ * compiling unionBedGraphs.cpp
- Building in src/windowBed
* compiling windowMain.cpp
* compiling windowBed.cpp
-
- Building in src/windowMaker
* compiling windowMakerMain.cpp
* compiling windowMaker.cpp
-
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
-make[1]: Leaving directory `/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0'
+make[1]: Leaving directory `/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
+ rm -f debian/bedtools.substvars
+ rm -f debian/bedtools.*.debhelper
+ rm -rf debian/bedtools/
dh_installdirs -A
+ install -d debian/bedtools
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -676,6 +678,12 @@ DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install targe
Adding cdbs dependencies to debian/bedtools.substvars
dh_installdirs -pbedtools
dh_installdocs -pbedtools
+ install -g 0 -o 0 -d debian/bedtools/usr/share/doc/bedtools
+ cp -a README.rst debian/bedtools/usr/share/doc/bedtools
+ chown -R 0:0 debian/bedtools/usr/share/doc
+ chmod -R go=rX debian/bedtools/usr/share/doc
+ chmod -R u\+rw debian/bedtools/usr/share/doc
+ install -g 0 -o 0 -m 644 -p debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright
dh_installexamples -pbedtools
dh_installman -pbedtools
dh_installinfo -pbedtools
@@ -683,83 +691,155 @@ dh_installmenu -pbedtools
dh_installcron -pbedtools
dh_installinit -pbedtools
dh_installdebconf -pbedtools
+ install -o 0 -g 0 -d debian/bedtools/DEBIAN
dh_installemacsen -pbedtools
dh_installcatalogs -pbedtools
+ grep -s -v '^misc:Depends=' debian/bedtools.substvars > debian/bedtools.substvars.new || true
+ mv debian/bedtools.substvars.new debian/bedtools.substvars
dh_installpam -pbedtools
dh_installlogrotate -pbedtools
dh_installlogcheck -pbedtools
dh_installchangelogs -pbedtools RELEASE_HISTORY
+ install -o 0 -g 0 -p -m644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian
+ install -o 0 -g 0 -p -m644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog
dh_installudev -pbedtools
dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
+ install -d debian/bedtools/usr/bin
+ cp -a ./bin/annotateBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToBed debian/bedtools/usr/bin/
+ cp -a ./bin/bamToFastq debian/bedtools/usr/bin/
+ cp -a ./bin/bed12ToBed6 debian/bedtools/usr/bin/
+ cp -a ./bin/bedpeToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToBam debian/bedtools/usr/bin/
+ cp -a ./bin/bedToIgv debian/bedtools/usr/bin/
+ cp -a ./bin/bedtools debian/bedtools/usr/bin/
+ cp -a ./bin/closestBed debian/bedtools/usr/bin/
+ cp -a ./bin/clusterBed debian/bedtools/usr/bin/
+ cp -a ./bin/complementBed debian/bedtools/usr/bin/
+ cp -a ./bin/coverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/expandCols debian/bedtools/usr/bin/
+ cp -a ./bin/fastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/flankBed debian/bedtools/usr/bin/
+ cp -a ./bin/genomeCoverageBed debian/bedtools/usr/bin/
+ cp -a ./bin/getOverlap debian/bedtools/usr/bin/
+ cp -a ./bin/groupBy debian/bedtools/usr/bin/
+ cp -a ./bin/intersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/linksBed debian/bedtools/usr/bin/
+ cp -a ./bin/mapBed debian/bedtools/usr/bin/
+ cp -a ./bin/maskFastaFromBed debian/bedtools/usr/bin/
+ cp -a ./bin/mergeBed debian/bedtools/usr/bin/
+ cp -a ./bin/multiBamCov debian/bedtools/usr/bin/
+ cp -a ./bin/multiIntersectBed debian/bedtools/usr/bin/
+ cp -a ./bin/nucBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToBed debian/bedtools/usr/bin/
+ cp -a ./bin/pairToPair debian/bedtools/usr/bin/
+ cp -a ./bin/randomBed debian/bedtools/usr/bin/
+ cp -a ./bin/shuffleBed debian/bedtools/usr/bin/
+ cp -a ./bin/slopBed debian/bedtools/usr/bin/
+ cp -a ./bin/sortBed debian/bedtools/usr/bin/
+ cp -a ./bin/subtractBed debian/bedtools/usr/bin/
+ cp -a ./bin/tagBam debian/bedtools/usr/bin/
+ cp -a ./bin/unionBedGraphs debian/bedtools/usr/bin/
+ cp -a ./bin/windowBed debian/bedtools/usr/bin/
+ cp -a ./bin/windowMaker debian/bedtools/usr/bin/
+ install -d debian/bedtools/usr/share/bedtools
+ cp -a ./genomes debian/bedtools/usr/share/bedtools/
dh_link -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
+ strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools
dh_compress -pbedtools
+ cd debian/bedtools
+ chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian
+ cd '/build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1'
dh_fixperms -pbedtools
+ find debian/bedtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/bedtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/bedtools/usr/share/doc -type f ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
+ find debian/bedtools/usr/share/man debian/bedtools/usr/man/ debian/bedtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/bedtools/usr/lib/perl5 debian/bedtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/bedtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
+ find debian/bedtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_makeshlibs -pbedtools
-rm /build/buildd-bedtools_2.15.0-1-sparc-zDCFqL/bedtools-2.15.0/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
+ rm -f debian/bedtools/DEBIAN/shlibs
+rm /build/buildd-bedtools_2.16.1-1-sparc-nx_0id/bedtools-2.16.1/debian/bedtools/usr/bin/groupBy # distributed in the filo package.
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
+ dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools
dh_gencontrol -pbedtools
+ echo misc:Depends= >> debian/bedtools.substvars
+ dpkg-gencontrol -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools
+ chmod 644 debian/bedtools/DEBIAN/control
+ chown 0:0 debian/bedtools/DEBIAN/control
dh_md5sums -pbedtools
+ (cd debian/bedtools >/dev/null ; find . -type f ! -regex '.*/DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 644 debian/bedtools/DEBIAN/md5sums
+ chown 0:0 debian/bedtools/DEBIAN/md5sums
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.15.0-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.15.0-1_sparc.changes
+ dpkg-deb -Z xz --build debian/bedtools ..
+dpkg-deb: building package `bedtools' in `../bedtools_2.16.1-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bedtools_2.16.1-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.15.0
+ dpkg-source --after-build bedtools-2.16.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120111-0734
+Build finished at 20120316-1340
-bedtools_2.15.0-1_sparc.changes:
+bedtools_2.16.1-1_sparc.changes:
Format: 1.8
-Date: Wed, 11 Jan 2012 15:07:45 +0900
+Date: Fri, 16 Mar 2012 19:06:49 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.15.0-1
+Version: 2.16.1-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
+Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.15.0-1) unstable; urgency=low
+ bedtools (2.16.1-1) unstable; urgency=low
.
- [3f8e754] Upstream version 2.15.0.
- [f27b295] Build-depend on python because of scripts/makeBashScripts.py.
- [2e3e8e8] Removed the /usr/bin/groupBy wrapper, as groupBy is also
- distributed by the filo package.
+ b7f2405 New upstream release.
+ 4add346 Corrected, updated and normalised Debian copyright.
+ 00b426d Conforms to Debian Policy 3.9.3.
+ 72c3c94 Verbose Debhelper.
Checksums-Sha1:
- d59c2b3055958af646c1578ed97f249f89a8df57 337630 bedtools_2.15.0-1_sparc.deb
+ 860dd1834056559f8993a4e9c507d71857a61984 372178 bedtools_2.16.1-1_sparc.deb
Checksums-Sha256:
- 1d5d08e93c70bba215e7f10da98f6eea75466268226643b3c779a63d66c5a55a 337630 bedtools_2.15.0-1_sparc.deb
+ ca34bfe51acdb131f200eb0d7e822f8aa2afb5b3607fa88c753335d451c4a64b 372178 bedtools_2.16.1-1_sparc.deb
Files:
- fc953b9d329a1e40fbaf2b5f4afc2b47 337630 science optional bedtools_2.15.0-1_sparc.deb
+ 36b9be3f55c5e6063ec38575a9ea028b 372178 science optional bedtools_2.16.1-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.15.0-1_sparc.deb
+bedtools_2.16.1-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 337630 bytes: control archive= 1865 bytes.
+ size 372178 bytes: control archive= 1974 bytes.
865 bytes, 19 lines control
- 2299 bytes, 40 lines md5sums
+ 2506 bytes, 44 lines md5sums
Package: bedtools
- Version: 2.15.0-1
+ Version: 2.16.1-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1289
+ Installed-Size: 1441
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -775,54 +855,58 @@ bedtools_2.15.0-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-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
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/bin/
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/expandCols
+-rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/closestBed
+-rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/complementBed
+-rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/randomBed
+-rwxr-xr-x root/root 36 2012-03-16 13:40 ./usr/bin/windowMaker
+-rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/flankBed
+-rwxr-xr-x root/root 36 2012-03-16 13:40 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/linksBed
+-rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 31 2012-03-16 13:40 ./usr/bin/windowBed
+-rwxr-xr-x root/root 1413812 2012-03-16 13:40 ./usr/bin/bedtools
+-rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/getOverlap
+-rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 29 2012-03-16 13:40 ./usr/bin/sortBed
+-rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/tagBam
+-rwxr-xr-x root/root 30 2012-03-16 13:40 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 34 2012-03-16 13:40 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 33 2012-03-16 13:40 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 32 2012-03-16 13:40 ./usr/bin/clusterBed
+-rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/nucBed
+-rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/bamToFastq
+-rwxr-xr-x root/root 28 2012-03-16 13:40 ./usr/bin/mapBed
+-rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 29 2012-03-16 13:40 ./usr/bin/slopBed
+-rwxr-xr-x root/root 35 2012-03-16 13:40 ./usr/bin/bedpeToBam
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11640 2012-03-13 13:10 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4827 2012-03-16 04:09 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 934 2012-03-16 10:08 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1505 2012-03-13 13:10 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2012-03-16 13:40 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2012-03-16 13:28 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2012-03-13 13:10 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 565 2012-03-13 13:10 ./usr/share/bedtools/genomes/mouse.mm8.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -836,7 +920,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-3e46963f-c9b5-4f65-adcc-b0d16c602978/build/buildd-bedtools_2.15.0-1-sparc-zDCFqL
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-a73b8fd2-7abf-4eca-8927-aaae67d24e71/build/buildd-bedtools_2.16.1-1-sparc-nx_0id
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -844,18 +928,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 70120
-Build-Time: 614
+Build-Space: 81448
+Build-Time: 741
Distribution: sid
-Install-Time: 99
-Job: bedtools_2.15.0-1
+Install-Time: 90
+Job: bedtools_2.16.1-1
Package: bedtools
-Package-Time: 768
-Source-Version: 2.15.0-1
-Space: 70120
+Package-Time: 891
+Source-Version: 2.16.1-1
+Space: 81448
Status: successful
-Version: 2.15.0-1
+Version: 2.16.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120111-0734
-Build needed 00:12:48, 70120k disc space
-Signature with key '4DF860F5' requested:
+Finished at 20120316-1340
+Build needed 00:14:51, 81448k disc space
+Signature with key '24E4F805' requested:
--
Suite of utilities for comparing genomic features.
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